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Mulet-Lazaro R, Delwel R. Oncogenic Enhancers in Leukemia. Blood Cancer Discov 2024; 5:303-317. [PMID: 39093124 PMCID: PMC11369600 DOI: 10.1158/2643-3230.bcd-23-0211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 06/06/2024] [Accepted: 07/17/2024] [Indexed: 08/04/2024] Open
Abstract
Although the study of leukemogenesis has traditionally focused on protein-coding genes, the role of enhancer dysregulation is becoming increasingly recognized. The advent of high-throughput sequencing, together with a better understanding of enhancer biology, has revealed how various genetic and epigenetic lesions produce oncogenic enhancers that drive transformation. These aberrations include translocations that lead to enhancer hijacking, point mutations that modulate enhancer activity, and copy number alterations that modify enhancer dosage. In this review, we describe these mechanisms in the context of leukemia and discuss potential therapeutic avenues to target these regulatory elements. Significance: Large-scale sequencing projects have uncovered recurrent gene mutations in leukemia, but the picture remains incomplete: some patients harbor no such aberrations, whereas others carry only a few that are insufficient to bring about transformation on their own. One of the missing pieces is enhancer dysfunction, which only recently has emerged as a critical driver of leukemogenesis. Knowledge of the various mechanisms of enhancer dysregulation is thus key for a complete understanding of leukemia and its causes, as well as the development of targeted therapies in the era of precision medicine.
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Affiliation(s)
- Roger Mulet-Lazaro
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
| | - Ruud Delwel
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
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2
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Nakamura M, Chonabayashi K, Narita M, Matsumura Y, Nishikawa M, Ochi Y, Nannya Y, Hishizawa M, Inoue D, Delwel R, Ogawa S, Takaori-Kondo A, Yoshida Y. Modelling and drug targeting of a myeloid neoplasm with atypical 3q26/MECOM rearrangement using patient-specific iPSCs. Br J Haematol 2024. [PMID: 39187468 DOI: 10.1111/bjh.19720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 08/11/2024] [Indexed: 08/28/2024]
Abstract
Structural variations involving enhancer hijacking induce aberrant oncogene expression and cause tumorigenesis. A rare translocation, t(3;8)(q26.2;q24), is associated with MECOM and MYC rearrangement, causing myeloid neoplasms with a dismal prognosis. The most recent World Health Organization classification recognises myeloid neoplasms with MECOM rearrangement as acute myeloid leukaemia (AML) with defining genetic abnormalities. Recently, the increasing use of induced pluripotent stem cell (iPSC) technology has helped elucidate the pathogenic processes of haematological malignancies. However, its utility for investigating enhancer hijacking in myeloid neoplasms remains unclear. In this study, we generated iPSC lines from patients with myelodysplastic syndromes (MDS) harbouring t(3;8)(q26.2;q24) and differentiated them into haematopoietic progenitor cells to model the pathophysiology of MDS with t(3;8)(q26.2;q24). Our iPSC model reproduced the primary patient's MECOM expression changes and histone H3 lysine 27 acetylation (H3K27ac) patterns in the MECOM promoter and MYC blood enhancer cluster (BENC). Furthermore, we revealed the apoptotic effects of the bromodomain and extra-terminal motif (BET) inhibitor on iPSC-derived MDS cells by suppressing activated MECOM. Our study demonstrates the usefulness of iPSC models for uncovering the precise mechanism of enhancer hijacking due to chromosomal structural changes and discovering potential therapeutic drug candidates for cancer treatment.
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Affiliation(s)
- Momoko Nakamura
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kazuhisa Chonabayashi
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Megumi Narita
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Yasuko Matsumura
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Misato Nishikawa
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Yotaro Ochi
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Division of Hematopoietic Disease Control, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Masakatsu Hishizawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Hematology, Kyoto-Katsura Hospital, Kyoto, Japan
| | - Daichi Inoue
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Ruud Delwel
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshinori Yoshida
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
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3
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Wu Q, Zhang Y, Yuan B, Huang Y, Jiang L, Liu F, Yan P, Cheng J, Long Z, Jiang X. Influence of genetic co-mutation on chemotherapeutic outcome in NPM1-mutated and FLT3-ITD wild-type AML patients. Cancer Med 2024; 13:e70102. [PMID: 39126219 PMCID: PMC11316012 DOI: 10.1002/cam4.70102] [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: 05/11/2024] [Revised: 07/27/2024] [Accepted: 08/04/2024] [Indexed: 08/12/2024] Open
Abstract
BACKGROUND Nucleophosmin 1 (NPM1) gene-mutated acute myeloid leukemia (NPM1mut AML) is classified as a subtype with a favorable prognosis. However, some patients fail to achieve a complete remission or relapse after intensified chemotherapy. Genetic abnormalities in concomitant mutations contribute to heterogeneous prognosis of NPM1mut AML patients. METHODS In this study, 91 NPM1-mutated and FLT3-ITD wild-type (NPM1mut/FLT3-ITDwt) AML patients with intermediate-risk karyotype were enrolled to analyze the impact of common genetic co-mutations on chemotherapeutic outcome. RESULTS Our data revealed that TET1/2 (52/91, 57.1%) was the most prevalent co-mutation in NPM1mut AML patients, followed by IDH1/2 (36/91, 39.6%), DNMT3A (35/91, 38.5%), myelodysplastic syndrome related genes (MDS-related genes) (ASXL1, BCOR, EZH2, RUNX1, SF3B1, SRSF2, STAG2, U2AF1 and ZRSR2 genes) (35/91, 38.5%), FLT3-TKD (27/91, 29.7%) and GATA2 (13/91, 14.3%) mutations. Patients with TET1/2mut exhibited significantly worse relapse-free survival (RFS) (median, 28.7 vs. not reached (NR) months; p = 0.0382) compared to patients with TET1/2wt, while no significant difference was observed in overall survival (OS) (median, NR vs. NR; p = 0.3035). GATA2mut subtype was associated with inferior OS (median, 28 vs. NR months; p < 0.0010) and RFS (median, 24 vs. NR months; p = 0.0224) compared to GATA2wt. By multivariate analysis, GATA2mut and MDS-related genesmut were independently associated with worse survival. CONCLUSION Mutations in TET1/2, GATA2 and MDS-related genes were found to significantly influence the chemotherapeutic outcome of patients with NPM1mut AML. The findings of our study have significant clinical implications for identifying patients who have an adverse response to frontline chemotherapy and provide a novel reference for further prognostic stratification of NPM1mut/FLT3-ITDwt AML patients.
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Affiliation(s)
- Quan Wu
- Department of Hematology, Nanfang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
| | - Yujiao Zhang
- Department of Hematology, Nanfang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
| | - Baoyi Yuan
- Department of Hematology, Nanfang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
| | - Yun Huang
- Department of Hematology, Nanfang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
| | - Ling Jiang
- Department of Hematology, Nanfang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
| | - Fang Liu
- Department of Hematology, Nanfang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
| | - Ping Yan
- Department of Hematology, Nanfang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
| | - Jiaying Cheng
- Department of Hematology, Nanfang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
| | - Zhiquan Long
- Department of Hematology, Nanfang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
| | - Xuejie Jiang
- Department of Hematology, Nanfang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
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4
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Pastoors D, Havermans M, Mulet-Lazaro R, Brian D, Noort W, Grasel J, Hoogenboezem R, Smeenk L, Demmers JAA, Milsom MD, Enver T, Groen RWJ, Bindels E, Delwel R. Oncogene EVI1 drives acute myeloid leukemia via a targetable interaction with CTBP2. SCIENCE ADVANCES 2024; 10:eadk9076. [PMID: 38748792 PMCID: PMC11095456 DOI: 10.1126/sciadv.adk9076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 04/10/2024] [Indexed: 05/19/2024]
Abstract
Acute myeloid leukemia (AML) driven by the activation of EVI1 due to chromosome 3q26/MECOM rearrangements is incurable. Because transcription factors such as EVI1 are notoriously hard to target, insight into the mechanism by which EVI1 drives myeloid transformation could provide alternative avenues for therapy. Applying protein folding predictions combined with proteomics technologies, we demonstrate that interaction of EVI1 with CTBP1 and CTBP2 via a single PLDLS motif is indispensable for leukemic transformation. A 4× PLDLS repeat construct outcompetes binding of EVI1 to CTBP1 and CTBP2 and inhibits proliferation of 3q26/MECOM rearranged AML in vitro and in xenotransplant models. This proof-of-concept study opens the possibility to target one of the most incurable forms of AML with specific EVI1-CTBP inhibitors. This has important implications for other tumor types with aberrant expression of EVI1 and for cancers transformed by different CTBP-dependent oncogenic transcription factors.
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Affiliation(s)
- Dorien Pastoors
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Marije Havermans
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Roger Mulet-Lazaro
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Duncan Brian
- Stem Cell Group, UCL Cancer Institute, University College London, London, UK
| | - Willy Noort
- Department of Hematology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Cancer Center Amsterdam, Cancer biology and immunology, Amsterdam, Netherlands
| | - Julius Grasel
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany
- Division of Experimental Hematology, German Cancer Research Center, DKFZ69120 Heidelberg, Germany
| | - Remco Hoogenboezem
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Leonie Smeenk
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | | | - Michael D. Milsom
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany
- Division of Experimental Hematology, German Cancer Research Center, DKFZ69120 Heidelberg, Germany
| | - Tariq Enver
- Stem Cell Group, UCL Cancer Institute, University College London, London, UK
| | - Richard W. J. Groen
- Department of Hematology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Cancer Center Amsterdam, Cancer biology and immunology, Amsterdam, Netherlands
| | - Eric Bindels
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Ruud Delwel
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
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5
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Hoffmeister LM, Suttorp J, Walter C, Antoniou E, Behrens YL, Göhring G, Awada A, von Neuhoff N, Reinhardt D, Schneider M. Panel-based RNA fusion sequencing improves diagnostics of pediatric acute myeloid leukemia. Leukemia 2024; 38:538-544. [PMID: 38086945 PMCID: PMC10912021 DOI: 10.1038/s41375-023-02102-9] [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: 07/21/2023] [Revised: 11/14/2023] [Accepted: 11/23/2023] [Indexed: 03/06/2024]
Abstract
New methods like panel-based RNA fusion sequencing (RNA-FS) promise improved diagnostics in various malignancies. We here analyzed the impact of RNA-FS on the initial diagnostics of 241 cases with pediatric acute myeloid leukemia (AML). We show that, compared to classical cytogenetics (CCG), RNA-FS reliably detected risk-relevant fusion genes in pediatric AML. In addition, RNA-FS strongly improved the detection of cryptic fusion genes like NUP98::NSD1, KMT2A::MLLT10 and CBFA2T3::GLIS2 and thereby resulted in an improved risk stratification in 25 patients (10.4%). Validation of additionally detected non-risk-relevant high confidence fusion calls identified PIM3::BRD1, C22orf34::BRD1, PSPC1::ZMYM2 and ARHGAP26::NR3C1 as common genetic variants and MYB::GATA1 as recurrent aberration, which we here describe in AML subtypes M0 and M7 for the first time. However, it failed to detect rare cytogenetically confirmed fusion events like MNX1::ETV6 and other chromosome 12p-abnormalities. As add-on benefit, the proportion of patients for whom measurable residual disease (MRD) monitoring became possible was increased by RNA-FS from 44.4 to 75.5% as the information on the fusion transcripts' sequence allowed the design of new MRD assays.
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Affiliation(s)
- Lina Marie Hoffmeister
- Department of Pediatric Hematology and Oncology, University Children's Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Julia Suttorp
- Department of Pediatric Hematology and Oncology, University Children's Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Christiane Walter
- Department of Pediatric Hematology and Oncology, University Children's Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Evangelia Antoniou
- Department of Pediatric Hematology and Oncology, University Children's Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Yvonne Lisa Behrens
- Department of Human Genetics, Hannover Medical School, 30625, Hannover, Germany
| | - Gudrun Göhring
- Department of Human Genetics, Hannover Medical School, 30625, Hannover, Germany
| | - Amani Awada
- Department of Pediatric Hematology and Oncology, University Children's Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Nils von Neuhoff
- Department of Pediatric Hematology and Oncology, University Children's Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Dirk Reinhardt
- Department of Pediatric Hematology and Oncology, University Children's Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Markus Schneider
- Department of Pediatric Hematology and Oncology, University Children's Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany.
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6
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Ng HL, Robinson ME, May PC, Innes AJ, Hiemeyer C, Feldhahn N. Promoter-centred chromatin interactions associated with EVI1 expression in EVI1+3q- myeloid leukaemia cells. Br J Haematol 2024; 204:945-958. [PMID: 38296260 DOI: 10.1111/bjh.19322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/17/2024]
Abstract
EVI1 expression is associated with poor prognosis in myeloid leukaemia, which can result from Chr.3q alterations that juxtapose enhancers to induce EVI1 expression via long-range chromatin interactions. More often, however, EVI1 expression occurs unrelated to 3q alterations, and it remained unclear if, in these cases, EVI1 expression is similarly caused by aberrant enhancer activation. Here, we report that, in EVI1+3q- myeloid leukaemia cells, the EVI1 promoter interacts via long-range chromatin interactions with promoters of distally located, active genes, rather than with enhancer elements. Unlike in 3q+ cells, EVI1 expression and long-range interactions appear to not depend on CTCF/cohesin, though EVI1+3q- cells utilise an EVI1 promoter-proximal site to enhance its expression that is also involved in CTCF-mediated looping in 3q+ cells. Long-range interactions in 3q- cells connect EVI1 to promoters of multiple genes, whose transcription correlates with EVI1 in EVI1+3q- cell lines, suggesting a shared mechanism of transcriptional regulation. In line with this, CRISPR interference-induced silencing of two of these sites minimally, but consistently reduced EVI1 expression. Together, we provide novel evidence of features associated with EVI1 expression in 3q- leukaemia and consolidate the view that EVI1 in 3q- leukaemia is largely promoter-driven, potentially involving long-distance promoter clustering.
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Affiliation(s)
- Han Leng Ng
- Department of Immunology and Inflammation, Faculty of Medicine, Centre for Haematology, Imperial College London, London, UK
| | - Mark E Robinson
- Department of Immunology and Inflammation, Faculty of Medicine, Centre for Haematology, Imperial College London, London, UK
- Center of Molecular and Cellular Oncology, Yale University, New Haven, Connecticut, USA
| | - Philippa C May
- Department of Immunology and Inflammation, Faculty of Medicine, Centre for Haematology, Imperial College London, London, UK
| | - Andrew J Innes
- Department of Immunology and Inflammation, Faculty of Medicine, Centre for Haematology, Imperial College London, London, UK
| | - Christina Hiemeyer
- Department of Immunology and Inflammation, Faculty of Medicine, Centre for Haematology, Imperial College London, London, UK
| | - Niklas Feldhahn
- Department of Immunology and Inflammation, Faculty of Medicine, Centre for Haematology, Imperial College London, London, UK
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7
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Snaith O, Poveda-Rogers C, Laczko D, Yang G, Morrissette JJD. Cytogenetics and genomics of acute myeloid leukemia. Best Pract Res Clin Haematol 2024; 37:101533. [PMID: 38490763 DOI: 10.1016/j.beha.2023.101533] [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: 02/28/2023] [Revised: 09/14/2023] [Accepted: 12/03/2023] [Indexed: 03/17/2024]
Abstract
The diversity of genetic and genomic abnormalities observed in acute myeloid leukemia (AML) reflects the complexity of these hematologic neoplasms. The detection of cytogenetic and molecular alterations is fundamental to diagnosis, risk stratification and treatment of AML. Chromosome rearrangements are well established in the diagnostic classification of AML, as are some gene mutations, in several international classification systems. Additionally, the detection of new mutational profiles at relapse and identification of mutations in the pre- and post-transplant settings are illuminating in understanding disease evolution and are relevant to the risk assessment of AML patients. In this review, we discuss recurrent cytogenetic abnormalities, as well as the detection of recurrent mutations, within the context of a normal karyotype, and in the setting of chromosome abnormalities. Two new classification schemes from the WHO and ICC are described, comparing these classifications in terms of diagnostic criteria and entity definition in AML. Finally, we discuss ways in which genomic sequencing can condense the detection of gene mutations and chromosome abnormalities into a single assay.
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Affiliation(s)
- Oraine Snaith
- Division of Hematopathology, Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Corey Poveda-Rogers
- Division of Precision and Computational Diagnostics, Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Dorottya Laczko
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Guang Yang
- Division of Precision and Computational Diagnostics, Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer J D Morrissette
- Division of Precision and Computational Diagnostics, Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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8
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Birdwell CE, Fiskus W, Kadia TM, Mill CP, Sasaki K, Daver N, DiNardo CD, Pemmaraju N, Borthakur G, Davis JA, Das K, Sharma S, Horrigan S, Ruan X, Su X, Khoury JD, Kantarjian H, Bhalla KN. Preclinical efficacy of targeting epigenetic mechanisms in AML with 3q26 lesions and EVI1 overexpression. Leukemia 2024; 38:545-556. [PMID: 38086946 DOI: 10.1038/s41375-023-02108-3] [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: 06/18/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 03/06/2024]
Abstract
AML with chromosomal alterations involving 3q26 overexpresses the transcription factor (TF) EVI1, associated with therapy refractoriness and inferior overall survival in AML. Consistent with a CRISPR screen highlighting BRD4 dependency, treatment with BET inhibitor (BETi) repressed EVI1, LEF1, c-Myc, c-Myb, CDK4/6, and MCL1, and induced apoptosis of AML cells with 3q26 lesions. Tegavivint (TV, BC-2059), known to disrupt the binding of nuclear β-catenin and TCF7L2/LEF1 with TBL1, also inhibited co-localization of EVI1 with TBL1 and dose-dependently induced apoptosis in AML cell lines and patient-derived (PD) AML cells with 3q26.2 lesions. TV treatment repressed EVI1, attenuated enhancer activity at ERG, TCF7L2, GATA2 and MECOM loci, abolished interactions between MYC enhancers, repressing AML stemness while upregulating mRNA gene-sets of interferon/inflammatory response, TGF-β signaling and apoptosis-regulation. Co-treatment with TV and BETi or venetoclax induced synergistic in vitro lethality and reduced AML burden, improving survival of NSG mice harboring xenografts of AML with 3q26.2 lesions.
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Affiliation(s)
| | - Warren Fiskus
- M.D. Anderson Cancer Center, The University of Texas, Houston, TX, 77030, USA
| | - Tapan M Kadia
- M.D. Anderson Cancer Center, The University of Texas, Houston, TX, 77030, USA
| | - Christopher P Mill
- M.D. Anderson Cancer Center, The University of Texas, Houston, TX, 77030, USA
| | - Koji Sasaki
- M.D. Anderson Cancer Center, The University of Texas, Houston, TX, 77030, USA
| | - Naval Daver
- M.D. Anderson Cancer Center, The University of Texas, Houston, TX, 77030, USA
| | - Courtney D DiNardo
- M.D. Anderson Cancer Center, The University of Texas, Houston, TX, 77030, USA
| | - Naveen Pemmaraju
- M.D. Anderson Cancer Center, The University of Texas, Houston, TX, 77030, USA
| | - Gautam Borthakur
- M.D. Anderson Cancer Center, The University of Texas, Houston, TX, 77030, USA
| | - John A Davis
- M.D. Anderson Cancer Center, The University of Texas, Houston, TX, 77030, USA
| | - Kaberi Das
- M.D. Anderson Cancer Center, The University of Texas, Houston, TX, 77030, USA
| | | | | | - Xinjia Ruan
- M.D. Anderson Cancer Center, The University of Texas, Houston, TX, 77030, USA
| | - Xiaoping Su
- M.D. Anderson Cancer Center, The University of Texas, Houston, TX, 77030, USA
| | - Joseph D Khoury
- University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Hagop Kantarjian
- M.D. Anderson Cancer Center, The University of Texas, Houston, TX, 77030, USA
| | - Kapil N Bhalla
- M.D. Anderson Cancer Center, The University of Texas, Houston, TX, 77030, USA.
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9
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Thoms JAI, Koch F, Raei A, Subramanian S, Wong JH, Vafaee F, Pimanda J. BloodChIP Xtra: an expanded database of comparative genome-wide transcription factor binding and gene-expression profiles in healthy human stem/progenitor subsets and leukemic cells. Nucleic Acids Res 2024; 52:D1131-D1137. [PMID: 37870453 PMCID: PMC10767868 DOI: 10.1093/nar/gkad918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/04/2023] [Accepted: 10/09/2023] [Indexed: 10/24/2023] Open
Abstract
The BloodChIP Xtra database (http://bloodchipXtra.vafaeelab.com/) facilitates genome-wide exploration and visualization of transcription factor (TF) occupancy and chromatin configuration in rare primary human hematopoietic stem (HSC-MPP) and progenitor (CMP, GMP, MEP) cells and acute myeloid leukemia (AML) cell lines (KG-1, ME-1, Kasumi1, TSU-1621-MT), along with chromatin accessibility and gene expression data from these and primary patient AMLs. BloodChIP Xtra features significantly more datasets than our earlier database BloodChIP (two primary cell types and two cell lines). Improved methodologies for determining TF occupancy and chromatin accessibility have led to increased availability of data for rare primary cell types across the spectrum of healthy and AML hematopoiesis. However, there is a continuing need for these data to be integrated in an easily accessible manner for gene-based queries and use in downstream applications. Here, we provide a user-friendly database based around genome-wide binding profiles of key hematopoietic TFs and histone marks in healthy stem/progenitor cell types. These are compared with binding profiles and chromatin accessibility derived from primary and cell line AML and integrated with expression data from corresponding cell types. All queries can be exported to construct TF-gene and protein-protein networks and evaluate the association of genes with specific cellular processes.
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Affiliation(s)
- Julie A I Thoms
- School of Biomedical Sciences, University of New South Wales, Sydney, Australia
| | - Forrest C Koch
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Alireza Raei
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Shruthi Subramanian
- School of Clinical Medicine, University of New South Wales, Sydney, Australia
| | - Jason W H Wong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Fatemeh Vafaee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- UNSW Data Science Hub, University of New South Wales, Sydney, Australia
| | - John E Pimanda
- School of Biomedical Sciences, University of New South Wales, Sydney, Australia
- School of Clinical Medicine, University of New South Wales, Sydney, Australia
- Haematology Department, Prince of Wales Hospital, Sydney, Australia
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10
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Knorr K, Rahman J, Erickson C, Wang E, Monetti M, Li Z, Ortiz-Pacheco J, Jones A, Lu SX, Stanley RF, Baez M, Fox N, Castro C, Marino AE, Jiang C, Penson A, Hogg SJ, Mi X, Nakajima H, Kunimoto H, Nishimura K, Inoue D, Greenbaum B, Knorr D, Ravetch J, Abdel-Wahab O. Systematic evaluation of AML-associated antigens identifies anti-U5 SNRNP200 therapeutic antibodies for the treatment of acute myeloid leukemia. NATURE CANCER 2023; 4:1675-1692. [PMID: 37872381 PMCID: PMC10733148 DOI: 10.1038/s43018-023-00656-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 09/19/2023] [Indexed: 10/25/2023]
Abstract
Despite recent advances in the treatment of acute myeloid leukemia (AML), there has been limited success in targeting surface antigens in AML, in part due to shared expression across malignant and normal cells. Here, high-density immunophenotyping of AML coupled with proteogenomics identified unique expression of a variety of antigens, including the RNA helicase U5 snRNP200, on the surface of AML cells but not on normal hematopoietic precursors and skewed Fc receptor distribution in the AML immune microenvironment. Cell membrane localization of U5 snRNP200 was linked to surface expression of the Fcγ receptor IIIA (FcγIIIA, also known as CD32A) and correlated with expression of interferon-regulated immune response genes. Anti-U5 snRNP200 antibodies engaging activating Fcγ receptors were efficacious across immunocompetent AML models and were augmented by combination with azacitidine. These data provide a roadmap of AML-associated antigens with Fc receptor distribution in AML and highlight the potential for targeting the AML cell surface using Fc-optimized therapeutics.
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Affiliation(s)
- Katherine Knorr
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Laboratory of Molecular Genetics and Immunology, Rockefeller University, New York, NY, USA
| | - Jahan Rahman
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Caroline Erickson
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eric Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Mara Monetti
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhuoning Li
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juliana Ortiz-Pacheco
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew Jones
- Laboratory of Molecular Genetics and Immunology, Rockefeller University, New York, NY, USA
| | - Sydney X Lu
- Stanford University School of Medicine, Stanford, CA, USA
| | - Robert F Stanley
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Baez
- Laboratory of Molecular Genetics and Immunology, Rockefeller University, New York, NY, USA
| | - Nina Fox
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cynthia Castro
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alessandra E Marino
- Laboratory of Molecular Genetics and Immunology, Rockefeller University, New York, NY, USA
| | - Caroline Jiang
- Laboratory of Molecular Genetics and Immunology, Rockefeller University, New York, NY, USA
| | - Alex Penson
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simon J Hogg
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xiaoli Mi
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hideaki Nakajima
- Department of Stem Cell and Immune Regulation, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Hiroyoshi Kunimoto
- Department of Stem Cell and Immune Regulation, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Koutarou Nishimura
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Japan
| | - Daichi Inoue
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Japan
| | - Benjamin Greenbaum
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Physiology, Biophysics & Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
| | - David Knorr
- Laboratory of Molecular Genetics and Immunology, Rockefeller University, New York, NY, USA
| | - Jeffrey Ravetch
- Laboratory of Molecular Genetics and Immunology, Rockefeller University, New York, NY, USA.
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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11
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Peters IJA, de Pater E, Zhang W. The role of GATA2 in adult hematopoiesis and cell fate determination. Front Cell Dev Biol 2023; 11:1250827. [PMID: 38033856 PMCID: PMC10682726 DOI: 10.3389/fcell.2023.1250827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023] Open
Abstract
The correct maintenance and differentiation of hematopoietic stem cells (HSC) in bone marrow is vital for the maintenance and operation of the human blood system. GATA2 plays a critical role in the maintenance of HSCs and the specification of HSCs into the different hematopoietic lineages, highlighted by the various defects observed in patients with heterozygous mutations in GATA2, resulting in cytopenias, bone marrow failure and increased chance of myeloid malignancy, termed GATA2 deficiency syndrome. Despite this, the mechanisms underlying GATA2 deficiency syndrome remain to be elucidated. The detailed description of how GATA2 regulates HSC maintenance and blood lineage determination is crucial to unravel the pathogenesis of GATA2 deficiency syndrome. In this review, we summarize current advances in elucidating the role of GATA2 in hematopoietic cell fate determination and discuss the challenges of modeling GATA2 deficiency syndrome.
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Affiliation(s)
| | | | - Wei Zhang
- *Correspondence: Wei Zhang, ; Emma de Pater,
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12
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Blakemore C, Damodharan S, Puccetti D. Inv(3) Acute Myeloid Leukemia in a Young Adult and Review of the Literature. Case Rep Oncol Med 2023; 2023:6628492. [PMID: 38026762 PMCID: PMC10657244 DOI: 10.1155/2023/6628492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
Acute myeloid leukemia (AML) with the high-risk variant inv(3)/t(3;3) or t(3;3)(q21;26.2) is rarely seen in the pediatric and young adult population. It is associated with poor outcomes with ineffective therapeutic options. Here, we present a case of an 18-year-old female with treatment refractory inv(3) AML in whom remission was unable to be obtained. Better treatment options are needed given the increased resistance to traditional therapy this subtype portrays. Here, we review the literature on pediatric and young adult inv(3) AML along with newer therapeutic options.
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Affiliation(s)
- Carlee Blakemore
- Department of Pediatrics, University of Wisconsin School of Medicine & Public Health, Madison, WI, USA
| | - Sudarshawn Damodharan
- Department of Pediatrics, University of Wisconsin School of Medicine & Public Health, Madison, WI, USA
- Division of Pediatric Hematology, Oncology and Bone Marrow Transplant, University of Wisconsin School of Medicine & Public Health, Madison, WI, USA
| | - Diane Puccetti
- Department of Pediatrics, University of Wisconsin School of Medicine & Public Health, Madison, WI, USA
- Division of Pediatric Hematology, Oncology and Bone Marrow Transplant, University of Wisconsin School of Medicine & Public Health, Madison, WI, USA
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13
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Mulet-Lazaro R, Delwel R. From Genotype to Phenotype: How Enhancers Control Gene Expression and Cell Identity in Hematopoiesis. Hemasphere 2023; 7:e969. [PMID: 37953829 PMCID: PMC10635615 DOI: 10.1097/hs9.0000000000000969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/11/2023] [Indexed: 11/14/2023] Open
Abstract
Blood comprises a wide array of specialized cells, all of which share the same genetic information and ultimately derive from the same precursor, the hematopoietic stem cell (HSC). This diversity of phenotypes is underpinned by unique transcriptional programs gradually acquired in the process known as hematopoiesis. Spatiotemporal regulation of gene expression depends on many factors, but critical among them are enhancers-sequences of DNA that bind transcription factors and increase transcription of genes under their control. Thus, hematopoiesis involves the activation of specific enhancer repertoires in HSCs and their progeny, driving the expression of sets of genes that collectively determine morphology and function. Disruption of this tightly regulated process can have catastrophic consequences: in hematopoietic malignancies, dysregulation of transcriptional control by enhancers leads to misexpression of oncogenes that ultimately drive transformation. This review attempts to provide a basic understanding of enhancers and their role in transcriptional regulation, with a focus on normal and malignant hematopoiesis. We present examples of enhancers controlling master regulators of hematopoiesis and discuss the main mechanisms leading to enhancer dysregulation in leukemia and lymphoma.
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Affiliation(s)
- Roger Mulet-Lazaro
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Ruud Delwel
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
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14
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Subramanian S, Thoms JAI, Huang Y, Cornejo-Páramo P, Koch FC, Jacquelin S, Shen S, Song E, Joshi S, Brownlee C, Woll PS, Chacon-Fajardo D, Beck D, Curtis DJ, Yehson K, Antonenas V, O'Brien T, Trickett A, Powell JA, Lewis ID, Pitson SM, Gandhi MK, Lane SW, Vafaee F, Wong ES, Göttgens B, Alinejad-Rokny H, Wong JWH, Pimanda JE. Genome-wide transcription factor-binding maps reveal cell-specific changes in the regulatory architecture of human HSPCs. Blood 2023; 142:1448-1462. [PMID: 37595278 PMCID: PMC10651876 DOI: 10.1182/blood.2023021120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/06/2023] [Accepted: 07/25/2023] [Indexed: 08/20/2023] Open
Abstract
Hematopoietic stem and progenitor cells (HSPCs) rely on a complex interplay among transcription factors (TFs) to regulate differentiation into mature blood cells. A heptad of TFs (FLI1, ERG, GATA2, RUNX1, TAL1, LYL1, LMO2) bind regulatory elements in bulk CD34+ HSPCs. However, whether specific heptad-TF combinations have distinct roles in regulating hematopoietic differentiation remains unknown. We mapped genome-wide chromatin contacts (HiC, H3K27ac, HiChIP), chromatin modifications (H3K4me3, H3K27ac, H3K27me3) and 10 TF binding profiles (heptad, PU.1, CTCF, STAG2) in HSPC subsets (stem/multipotent progenitors plus common myeloid, granulocyte macrophage, and megakaryocyte erythrocyte progenitors) and found TF occupancy and enhancer-promoter interactions varied significantly across cell types and were associated with cell-type-specific gene expression. Distinct regulatory elements were enriched with specific heptad-TF combinations, including stem-cell-specific elements with ERG, and myeloid- and erythroid-specific elements with combinations of FLI1, RUNX1, GATA2, TAL1, LYL1, and LMO2. Furthermore, heptad-occupied regions in HSPCs were subsequently bound by lineage-defining TFs, including PU.1 and GATA1, suggesting that heptad factors may prime regulatory elements for use in mature cell types. We also found that enhancers with cell-type-specific heptad occupancy shared a common grammar with respect to TF binding motifs, suggesting that combinatorial binding of TF complexes was at least partially regulated by features encoded in DNA sequence motifs. Taken together, this study comprehensively characterizes the gene regulatory landscape in rare subpopulations of human HSPCs. The accompanying data sets should serve as a valuable resource for understanding adult hematopoiesis and a framework for analyzing aberrant regulatory networks in leukemic cells.
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Affiliation(s)
- Shruthi Subramanian
- School of Clinical Medicine, University of New South Wales, Sydney, Australia
| | - Julie A. I. Thoms
- School of Biomedical Sciences, University of New South Wales, Sydney, Australia
| | - Yizhou Huang
- Centre for Health Technologies and the School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | | | - Forrest C. Koch
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, Australia
| | | | - Sylvie Shen
- Bone Marrow Transplant Laboratory, NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Emma Song
- Bone Marrow Transplant Laboratory, NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Swapna Joshi
- School of Clinical Medicine, University of New South Wales, Sydney, Australia
| | - Chris Brownlee
- Mark Wainwright Analytical Centre, University of New South Wales, Sydney, Australia
| | - Petter S. Woll
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Diego Chacon-Fajardo
- Centre for Health Technologies and the School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - Dominik Beck
- Centre for Health Technologies and the School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - David J. Curtis
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | - Kenneth Yehson
- Blood Transplant and Cell Therapies Laboratory, NSW Health Pathology, Westmead, NSW, Australia
| | - Vicki Antonenas
- Blood Transplant and Cell Therapies Laboratory, NSW Health Pathology, Westmead, NSW, Australia
| | | | - Annette Trickett
- Bone Marrow Transplant Laboratory, NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Jason A. Powell
- Centre for Cancer Biology, SA Pathology, University of South Australia, Adelaide, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, Australia
| | - Ian D. Lewis
- Centre for Cancer Biology, SA Pathology, University of South Australia, Adelaide, Australia
| | - Stuart M. Pitson
- Centre for Cancer Biology, SA Pathology, University of South Australia, Adelaide, Australia
| | - Maher K. Gandhi
- Blood Cancer Research Group, Mater Research, The University of Queensland, Brisbane, QLD, Australia
| | - Steven W. Lane
- Cancer Program, QIMR Berghofer Medical Research, Brisbane, Australia
| | - Fatemeh Vafaee
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, Australia
- UNSW Data Science Hub, University of New South Wales, Sydney, Australia
| | - Emily S. Wong
- Victor Chang Cardiac Research Institute, Sydney, Australia
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, Australia
| | - Berthold Göttgens
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
| | - Hamid Alinejad-Rokny
- BioMedical Machine Learning Lab, Graduate School of Biomedical Engineering, University of New South Wales, Sydney, Australia
| | - Jason W. H. Wong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - John E. Pimanda
- School of Clinical Medicine, University of New South Wales, Sydney, Australia
- School of Biomedical Sciences, University of New South Wales, Sydney, Australia
- Haematology Department, Prince of Wales Hospital, Sydney, Australia
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15
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West RR, Bauer TR, Tuschong LM, Embree LJ, Calvo KR, Tillo D, Davis J, Holland SM, Hickstein DD. A novel GATA2 distal enhancer mutation results in MonoMAC syndrome in 2 second cousins. Blood Adv 2023; 7:6351-6363. [PMID: 37595058 PMCID: PMC10587712 DOI: 10.1182/bloodadvances.2023010458] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/24/2023] [Accepted: 08/12/2023] [Indexed: 08/20/2023] Open
Abstract
Mutations in the transcription factor GATA2 can cause MonoMAC syndrome, a GATA2 deficiency disease characterized by several findings, including disseminated nontuberculous mycobacterial infections, severe deficiencies of monocytes, natural killer cells, and B lymphocytes, and myelodysplastic syndrome. GATA2 mutations are found in ∼90% of patients with a GATA2 deficiency phenotype and are largely missense mutations in the conserved second zinc-finger domain. Mutations in an intron 5 regulatory enhancer element are also well described in GATA2 deficiency. Here, we present a multigeneration kindred with the clinical features of GATA2 deficiency but lacking an apparent GATA2 mutation. Whole genome sequencing revealed a unique adenine-to-thymine variant in the GATA2 -110 enhancer 116,855 bp upstream of the GATA2 ATG start site. The mutation creates a new E-box consensus in position with an existing GATA-box to generate a new hematopoietic regulatory composite element. The mutation segregates with the disease in several generations of the family. Cell type-specific allelic imbalance of GATA2 expression was observed in the bone marrow of a patient with higher expression from the mutant-linked allele. Allele-specific overexpression of GATA2 was observed in CRISPR/Cas9-modified HL-60 cells and in luciferase assays with the enhancer mutation. This study demonstrates overexpression of GATA2 resulting from a single nucleotide change in an upstream enhancer element in patients with MonoMAC syndrome. Patients in this study were enrolled in the National Institute of Allergy and Infectious Diseases clinical trial and the National Cancer Institute clinical trial (both trials were registered at www.clinicaltrials.gov as #NCT01905826 and #NCT01861106, respectively).
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Affiliation(s)
- Robert R. West
- Immune Deficiency–Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Thomas R. Bauer
- Immune Deficiency–Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Laura M. Tuschong
- Immune Deficiency–Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Lisa J. Embree
- Immune Deficiency–Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Katherine R. Calvo
- Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, MD
| | - Desiree Tillo
- Genomics Core, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Joie Davis
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Steven M. Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Dennis D. Hickstein
- Immune Deficiency–Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
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16
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Heyes E, Wilhelmson AS, Wenzel A, Manhart G, Eder T, Schuster MB, Rzepa E, Pundhir S, D'Altri T, Frank AK, Gentil C, Woessmann J, Schoof EM, Meggendorfer M, Schwaller J, Haferlach T, Grebien F, Porse BT. TET2 lesions enhance the aggressiveness of CEBPA-mutant acute myeloid leukemia by rebalancing GATA2 expression. Nat Commun 2023; 14:6185. [PMID: 37794021 PMCID: PMC10550934 DOI: 10.1038/s41467-023-41927-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 09/22/2023] [Indexed: 10/06/2023] Open
Abstract
The myeloid transcription factor CEBPA is recurrently biallelically mutated (i.e., double mutated; CEBPADM) in acute myeloid leukemia (AML) with a combination of hypermorphic N-terminal mutations (CEBPANT), promoting expression of the leukemia-associated p30 isoform, and amorphic C-terminal mutations. The most frequently co-mutated genes in CEBPADM AML are GATA2 and TET2, however the molecular mechanisms underlying this co-mutational spectrum are incomplete. By combining transcriptomic and epigenomic analyses of CEBPA-TET2 co-mutated patients with models thereof, we identify GATA2 as a conserved target of the CEBPA-TET2 mutational axis, providing a rationale for the mutational spectra in CEBPADM AML. Elevated CEBPA levels, driven by CEBPANT, mediate recruitment of TET2 to the Gata2 distal hematopoietic enhancer thereby increasing Gata2 expression. Concurrent loss of TET2 in CEBPADM AML induces a competitive advantage by increasing Gata2 promoter methylation, thereby rebalancing GATA2 levels. Of clinical relevance, demethylating treatment of Cebpa-Tet2 co-mutated AML restores Gata2 levels and prolongs disease latency.
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Affiliation(s)
- Elizabeth Heyes
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria
| | - Anna S Wilhelmson
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anne Wenzel
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gabriele Manhart
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria
| | - Thomas Eder
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria
| | - Mikkel B Schuster
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Edwin Rzepa
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria
| | - Sachin Pundhir
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Teresa D'Altri
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anne-Katrine Frank
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Coline Gentil
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Woessmann
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Erwin M Schoof
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | - Jürg Schwaller
- Department of Biomedicine, University Children's Hospital Basel, Basel, Switzerland
| | | | - Florian Grebien
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria.
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.
| | - Bo T Porse
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark.
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
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17
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Auger N, Douet-Guilbert N, Quessada J, Theisen O, Lafage-Pochitaloff M, Troadec MB. Cytogenetics in the management of myelodysplastic neoplasms (myelodysplastic syndromes, MDS): Guidelines from the groupe francophone de cytogénétique hématologique (GFCH). Curr Res Transl Med 2023; 71:103409. [PMID: 38091642 DOI: 10.1016/j.retram.2023.103409] [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: 07/10/2023] [Revised: 09/04/2023] [Accepted: 09/14/2023] [Indexed: 12/26/2023]
Abstract
Myelodysplastic neoplasms (MDS) are clonal hematopoietic neoplasms. Chromosomal abnormalities (CAs) are detected in 40-45% of de novo MDS and up to 80% of post-cytotoxic therapy MDS (MDS-pCT). Lately, several changes appeared in World Health Organization (WHO) classification and International Consensus Classification (ICC). The novel 'biallelic TP53 inactivation' (also called 'multi-hit TP53') MDS entity requires systematic investigation of TP53 locus (17p13.1). The ICC maintains CA allowing the diagnosis of MDS without dysplasia (del(5q), del(7q), -7 and complex karyotype). Deletion 5q is the only CA, still representing a low blast class of its own, if isolated or associated with one additional CA other than -7 or del(7q) and without multi-hit TP53. It represents one of the most frequent aberrations in adults' MDS, with chromosome 7 aberrations, and trisomy 8. Conversely, translocations are rarer in MDS. In children, del(5q) is very rare while -7 and del(7q) are predominant. Identification of a germline predisposition is key in childhood MDS. Aberrations of chromosomes 5, 7 and 17 are the most frequent in MDS-pCT, grouped in complex karyotypes. Despite the ever-increasing importance of molecular features, cytogenetics remains a major part of diagnosis and prognosis. In 2022, a molecular international prognostic score (IPSS-M) was proposed, combining the prognostic value of mutated genes to the previous scoring parameters (IPSS-R) including cytogenetics, still essential. A karyotype on bone marrow remains mandatory at diagnosis of MDS with complementary molecular analyses now required. Analyses with FISH or other technologies providing similar information can be necessary to complete and help in case of karyotype failure, for doubtful CA, for clonality assessment, and for detection of TP53 deletion to assess TP53 biallelic alterations.
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Affiliation(s)
- Nathalie Auger
- Gustave Roussy, Génétique des tumeurs, 144 rue Edouard Vaillant, Villejuif 94805, France
| | - Nathalie Douet-Guilbert
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest F-29200, France; CHRU Brest, Laboratoire de Génétique Chromosomique, Service de génétique, Brest, France
| | - Julie Quessada
- Laboratoire de Cytogénétique Hématologique, CHU Timone Aix Marseille University, Marseille, France
| | - Olivier Theisen
- Hematology Biology, Nantes University Hospital, Nantes, France
| | | | - Marie-Bérengère Troadec
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest F-29200, France; CHRU Brest, Laboratoire de Génétique Chromosomique, Service de génétique, Brest, France.
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18
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Lux S, Milsom MD. EVI1-mediated Programming of Normal and Malignant Hematopoiesis. Hemasphere 2023; 7:e959. [PMID: 37810550 PMCID: PMC10553128 DOI: 10.1097/hs9.0000000000000959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/14/2023] [Indexed: 10/10/2023] Open
Abstract
Ecotropic viral integration site 1 (EVI1), encoded at the MECOM locus, is an oncogenic zinc finger transcription factor with diverse roles in normal and malignant cells, most extensively studied in the context of hematopoiesis. EVI1 interacts with other transcription factors in a context-dependent manner and regulates transcription and chromatin remodeling, thereby influencing the proliferation, differentiation, and survival of cells. Interestingly, it can act both as a transcriptional activator as well as a transcriptional repressor. EVI1 is expressed, and fulfills important functions, during the development of different tissues, including the nervous system and hematopoiesis, demonstrating a rigid spatial and temporal expression pattern. However, EVI1 is regularly overexpressed in a variety of cancer entities, including epithelial cancers such as ovarian and pancreatic cancer, as well as in hematologic malignancies like myeloid leukemias. Importantly, EVI1 overexpression is generally associated with a very poor clinical outcome and therapy-resistance. Thus, EVI1 is an interesting candidate to study to improve the prognosis and treatment of high-risk patients with "EVI1high" hematopoietic malignancies.
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Affiliation(s)
- Susanne Lux
- Division of Experimental Hematology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael D. Milsom
- Division of Experimental Hematology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
- DKFZ-ZMBH Alliance, Heidelberg, Germany
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19
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Aktar A, Heit B. Role of the pioneer transcription factor GATA2 in health and disease. J Mol Med (Berl) 2023; 101:1191-1208. [PMID: 37624387 DOI: 10.1007/s00109-023-02359-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 08/04/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023]
Abstract
The transcription factor GATA2 is involved in human diseases ranging from hematopoietic disorders, to cancer, to infectious diseases. GATA2 is one of six GATA-family transcription factors that act as pioneering transcription factors which facilitate the opening of heterochromatin and the subsequent binding of other transcription factors to induce gene expression from previously inaccessible regions of the genome. Although GATA2 is essential for hematopoiesis and lymphangiogenesis, it is also expressed in other tissues such as the lung, prostate gland, gastrointestinal tract, central nervous system, placenta, fetal liver, and fetal heart. Gene or transcriptional abnormalities of GATA2 causes or predisposes patients to several diseases including the hematological cancers acute myeloid leukemia and acute lymphoblastic leukemia, the primary immunodeficiency MonoMAC syndrome, and to cancers of the lung, prostate, uterus, kidney, breast, gastric tract, and ovaries. Recent data has also linked GATA2 expression and mutations to responses to infectious diseases including SARS-CoV-2 and Pneumocystis carinii pneumonia, and to inflammatory disorders such as atherosclerosis. In this article we review the role of GATA2 in the etiology and progression of these various diseases.
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Affiliation(s)
- Amena Aktar
- Department of Microbiology and Immunology; the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, ON, N6A 5C1, Canada
| | - Bryan Heit
- Department of Microbiology and Immunology; the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, ON, N6A 5C1, Canada.
- Robarts Research Institute, London, ON, N6A 3K7, Canada.
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20
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Ratajczak B, Przybyłowicz-Chalecka A, Czerwińska-Rybak J, Kanduła Z, Ustaszewski A, Gil L, Lewandowski K, Jarmuż-Szymczak M. The presence of additional cytogenetic aberrations in chronic myeloid leukemia cells at the time of diagnosis or their appearance on tyrosine kinase inhibitor therapy predicts the imatinib treatment failure. Leuk Res 2023; 132:107349. [PMID: 37393627 DOI: 10.1016/j.leukres.2023.107349] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/04/2023]
Abstract
Currently used treatment of CML dramatically improved the prognosis of disease. However, additional chromosome aberrations (ACA/Ph+) are still one of the adverse prognostic factors. OBJECTIVES evaluation of the impact of ACA/Ph+ appearance during disease outcome on the response to treatment. THE STUDY GROUP: consisted of 203 patients. The median time of follow-up was 72 months. ACA/Ph+ was found in 53 patients. RESULTS patients were divided into four groups: standard risk, intermediate, high and very high risk. When ACA/Ph+ presence was documented at diagnosis time the optimal response was observed in 41.2%, 25%, and 0% of pts with intermediate, high and very high risk, respectively. If ACA/Ph+ were detected during imatinib treatment the optimal response was in 4.8% of patients. The risk of blastic transformation for patients with standard risk, intermediate, high and very high risk was 2.7%, 18.4%, 20% and 50%, respectively. CONCLUSIONS the presence of ACA/Ph+ at diagnosis time or their appearance on therapy seems to be clinically relevant not only in terms of the risk of blastic transformation but also in terms of the treatment failure. Gathering patients with various karyotypes and their responses to treatment would allow to set better guidelines and predictions.
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Affiliation(s)
- Błażej Ratajczak
- Department of Haematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland.
| | - Anna Przybyłowicz-Chalecka
- Department of Haematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Joanna Czerwińska-Rybak
- Department of Haematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Zuzanna Kanduła
- Department of Haematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Adam Ustaszewski
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Lidia Gil
- Department of Haematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Krzysztof Lewandowski
- Department of Haematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Małgorzata Jarmuż-Szymczak
- Department of Haematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland; Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
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21
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Tanaka A, Nishimura K, Saika W, Kon A, Koike Y, Tatsumi H, Takeda J, Nomura M, Zang W, Nakayama M, Matsuda M, Yamazaki H, Fukumoto M, Ito H, Hayashi Y, Kitamura T, Kawamoto H, Takaori-Kondo A, Koseki H, Ogawa S, Inoue D. SETBP1 is dispensable for normal and malignant hematopoiesis. Leukemia 2023; 37:1802-1811. [PMID: 37464069 DOI: 10.1038/s41375-023-01970-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 06/23/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023]
Abstract
SETBP1 is a potential epigenetic regulator whose hotspot mutations preventing proteasomal degradation are recurrently detected in myeloid malignancies with poor prognosis. It is believed that the mutant SETBP1 exerts amplified effects of wild-type SETBP1 rather than neomorphic functions. This indicates that dysregulated quantitative control of SETBP1 would result in the transformation of hematopoietic cells. However, little is known about the roles of endogenous SETBP1 in malignant and normal hematopoiesis. Thus, we integrated the analyses of primary AML and healthy samples, cancer cell lines, and a newly generated murine model, Vav1-iCre;Setbp1fl/fl. Despite the expression in long-term hematopoietic stem cells, SETBP1 depletion in normal hematopoiesis minimally alters self-renewal, differentiation, or reconstitution in vivo. Indeed, its loss does not profoundly alter transcription or chromatin accessibilities. Furthermore, although AML with high SETBP1 mRNA is associated with genetic and clinical characteristics for dismal outcomes, SETBP1 is dispensable for the development or maintenance of AML. Contrary to the evidence that SETBP1 mutations are restricted to myeloid malignancies, dependency on SETBP1 mRNA expression is not observed in AML. These unexpected results shed light on the unrecognized idea that a physiologically nonessential gene can act as an oncogene when the machinery of protein degradation is damaged.
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Affiliation(s)
- Atsushi Tanaka
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Laboratory of Immunology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koutarou Nishimura
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Wataru Saika
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Department of Hematology, Shiga University of Medical Science, Shiga, Japan
| | - Ayana Kon
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yui Koike
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Hiromi Tatsumi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - June Takeda
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masaki Nomura
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Facility for iPS Cell Therapy, CiRA Foundation, Kyoto, Japan
| | - Weijia Zang
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Manabu Nakayama
- Laboratory of Medical Omics Research, Department of Frontier Research and Development, Kazusa DNA Research Institute, Kazusa-Kamatari, Kisarazu, Chiba, Japan
| | - Masashi Matsuda
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Hiromi Yamazaki
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Miki Fukumoto
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Hiromi Ito
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Yasutaka Hayashi
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Toshio Kitamura
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Hiroshi Kawamoto
- Laboratory of Immunology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Haruhiko Koseki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 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 (WPI-ASHBi), Kyoto University, Kyoto, Japan
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Daichi Inoue
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan.
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
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22
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Richard-Carpentier G, Rausch CR, Sasaki K, Hammond D, Morita K, Takahashi K, Tang G, Kanagal-Shamanna R, Bhalla K, Dinardo CD, Borthakur G, Pemmaraju N, Shpall EJ, Alousi A, Daver NG, Garcia-Manero G, Konopleva MY, Ravandi F, Kantarjian HM, Kadia TM. Characteristics and clinical outcomes of patients with acute myeloid leukemia with inv(3)(q21q26.2) or t(3;3)(q21;q26.2). Haematologica 2023; 108:2331-2342. [PMID: 36951163 PMCID: PMC10483357 DOI: 10.3324/haematol.2022.282030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 03/13/2023] [Indexed: 03/24/2023] Open
Abstract
Acute myeloid leukemia (AML) with inv(3)(q21q26.2)/t(3;3)(q21;q26.2) has a very poor prognosis. Determinants of clinical outcomes and optimal treatment remain uncertain. We retrospectively reviewed 108 cases of AML with inv(3)/t(3;3) and evaluated clinicopathological characteristics and clinical outcomes: 53 newly diagnosed (ND) AML and 55 relapsed/refractory (R/R) AML. Median age was 55 years. White blood cell (WBC) count ≥20x109/L and platelet count ≥140x109/L was observed in 25% and 32% of ND patients, respectively. Anomalies involving chromosome 7 were identified in 56% of patients. The most frequently mutated genes were SF3B1, PTPN11, NRAS, KRAS and ASXL1. In ND patients, the composite complete remission (CRc) rate was 46% overall; 46% with high-intensity treatments and 47% with lowintensity treatments. The 30-day mortality was 14% and 0%, with high- and low-intensity treatment, respectively. In R/R patients, the CRc rate was 14%. Venetoclax based-regimens were associated with a CRc rate of 33%. The 3-year overall survival (OS) was 8.8% and 7.1% in ND and R/R patients, respectively. The 3-year cumulative incidence of relapse was 81.7% overall. Older age, high WBC, high peripheral blast count, secondary AML and KRAS, ASXL1, DNMT3A mutations were associated with worse OS in univariable analyses. The 5-year OS rates were 44% and 6% with or without hematopoietic stem cell transplantation in CR1, respectively. AML with inv(3)/t(3;3) is associated with low CR rates, very high risk of relapse and dismal long-term survival. Intensive chemotherapy and hy pomethylating agents provide similar rates of remission and patients achieving CR benefit from hematopoietic stem cell transplantation in first CR.
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Affiliation(s)
- Guillaume Richard-Carpentier
- Department of Medicine, Division of Medical Oncology and Hematology, University of Toronto, Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Leukemia, Division of Cancer Medicine, University of Texas, MD Anderson Cancer Center, Houston, Texas.
| | - Caitlin R Rausch
- Division of Pharmacy, University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Koji Sasaki
- Department of Leukemia, Division of Cancer Medicine, University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Danielle Hammond
- Department of Leukemia, Division of Cancer Medicine, University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Kiyomi Morita
- Department of Leukemia, Division of Cancer Medicine, University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Koichi Takahashi
- Department of Leukemia, Division of Cancer Medicine, University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Guilin Tang
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Kapil Bhalla
- Department of Leukemia, Division of Cancer Medicine, University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Courtney D Dinardo
- Department of Leukemia, Division of Cancer Medicine, University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Gautam Borthakur
- Department of Leukemia, Division of Cancer Medicine, University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Naveen Pemmaraju
- Department of Leukemia, Division of Cancer Medicine, University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Elizabeth J Shpall
- Department of Stem Cell Transplantation and Cellular Therapy, Division of Cancer Medicine, University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Amin Alousi
- Department of Stem Cell Transplantation and Cellular Therapy, Division of Cancer Medicine, University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Naval G Daver
- Department of Leukemia, Division of Cancer Medicine, University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Guillermo Garcia-Manero
- Department of Leukemia, Division of Cancer Medicine, University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Marina Y Konopleva
- Department of Leukemia, Division of Cancer Medicine, University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Farhad Ravandi
- Department of Leukemia, Division of Cancer Medicine, University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Hagop M Kantarjian
- Department of Leukemia, Division of Cancer Medicine, University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Tapan M Kadia
- Department of Leukemia, Division of Cancer Medicine, University of Texas, MD Anderson Cancer Center, Houston, Texas.
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23
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Rein A, Geron I, Kugler E, Fishman H, Gottlieb E, Abramovich I, Giladi A, Amit I, Mulet-Lazaro R, Delwel R, Gröschel S, Levin-Zaidman S, Dezorella N, Holdengreber V, Rao TN, Yacobovich J, Steinberg-Shemer O, Huang QH, Tan Y, Chen SJ, Izraeli S, Birger Y. Cellular and metabolic characteristics of pre-leukemic hematopoietic progenitors with GATA2 haploinsufficiency. Haematologica 2023; 108:2316-2330. [PMID: 36475518 PMCID: PMC10483369 DOI: 10.3324/haematol.2022.279437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 12/01/2022] [Indexed: 09/08/2023] Open
Abstract
Mono-allelic germline disruptions of the transcription factor GATA2 result in a propensity for developing myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML), affecting more than 85% of carriers. How a partial loss of GATA2 functionality enables leukemic transformation years later is unclear. This question has remained unsolved mainly due to the lack of informative models, as Gata2 heterozygote mice do not develop hematologic malignancies. Here we show that two different germline Gata2 mutations (TgErg/Gata2het and TgErg/Gata2L359V) accelerate AML in mice expressing the human hematopoietic stem cell regulator ERG. Analysis of Erg/Gata2het fetal liver and bone marrow-derived hematopoietic cells revealed a distinct pre-leukemic phenotype. This was characterized by enhanced transition from stem to progenitor state, increased proliferation, and a striking mitochondrial phenotype, consisting of highly expressed oxidative-phosphorylation-related gene sets, elevated oxygen consumption rates, and notably, markedly distorted mitochondrial morphology. Importantly, the same mitochondrial gene-expression signature was observed in human AML harboring GATA2 aberrations. Similar to the observations in mice, non-leukemic bone marrows from children with germline GATA2 mutation demonstrated marked mitochondrial abnormalities. Thus, we observed the tumor suppressive effects of GATA2 in two germline Gata2 genetic mouse models. As oncogenic mutations often accumulate with age, GATA2 deficiency-mediated priming of hematopoietic cells for oncogenic transformation may explain the earlier occurrence of MDS/AML in patients with GATA2 germline mutation. The mitochondrial phenotype is a potential therapeutic opportunity for the prevention of leukemic transformation in these patients.
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Affiliation(s)
- Avigail Rein
- Department of Human Molecular Genetics and Biochemistry, Sackler Medical School, Aviv University, Aviv 69978, Israel; The Rina Zaizov Division of Pediatric Hematology-Oncology, Schneider Children's Medical Center, Petah Tikva; Israel; Functional Genomics and Childhood Leukaemia Research, Sheba Medical Centre, Tel-Hashomer
| | - Ifat Geron
- Department of Human Molecular Genetics and Biochemistry, Sackler Medical School, Aviv University, Aviv 69978, Israel; The Rina Zaizov Division of Pediatric Hematology-Oncology, Schneider Children's Medical Center, Petah Tikva; Israel; Functional Genomics and Childhood Leukaemia Research, Sheba Medical Centre, Tel-Hashomer, Israel; Felsenstein Medical Research Center, Sackler School of Medicine Tel-Aviv University, Petah Tikva
| | - Eitan Kugler
- Department of Human Molecular Genetics and Biochemistry, Sackler Medical School, Aviv University, Aviv 69978, Israel; The Rina Zaizov Division of Pediatric Hematology-Oncology, Schneider Children's Medical Center, Petah Tikva; Israel; Functional Genomics and Childhood Leukaemia Research, Sheba Medical Centre, Tel-Hashomer
| | - Hila Fishman
- Department of Human Molecular Genetics and Biochemistry, Sackler Medical School, Aviv University, Aviv 69978, Israel; The Rina Zaizov Division of Pediatric Hematology-Oncology, Schneider Children's Medical Center, Petah Tikva; Israel; Functional Genomics and Childhood Leukaemia Research, Sheba Medical Centre, Tel-Hashomer
| | - Eyal Gottlieb
- Technion Integrated Cancer Center, Faculty of Medicine, Technion Israel Institute of Technology, Haifa
| | - Ifat Abramovich
- Technion Integrated Cancer Center, Faculty of Medicine, Technion Israel Institute of Technology, Haifa
| | - Amir Giladi
- Department of Immunology, Weizmann Institute of Science, Rehovot
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot
| | - Roger Mulet-Lazaro
- Department of Hematology, Erasmus University Medical Center, Rotterdam, 3015 GE
| | - Ruud Delwel
- Department of Hematology, Erasmus University Medical Center, Rotterdam, 3015 GE, the Netherlands; Oncode Institute, Erasmus University Medical Center, Rotterdam
| | - Stefan Gröschel
- Department of Hematology, Erasmus University Medical Center, Rotterdam, 3015 GE, the Netherlands; Molecular Leukemogenesis, Deutsches Krebsforschungszentrum, 69120 Heidelberg, Germany; Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg
| | | | - Nili Dezorella
- Electron Microscopy Unit, Weizmann Institute of Science, Rehovot
| | - Vered Holdengreber
- Electron Microscopy Unit, IDRFU, Faculty of Life Sciences, Aviv University
| | - Tata Nageswara Rao
- Stem Cells and Leukemia Laboratory, University Clinic of Hematology and Central Hematology, Department of Biomedical Research (DBMR), Inselspital Bern, University of Bern
| | - Joanne Yacobovich
- The Rina Zaizov Division of Pediatric Hematology-Oncology, Schneider Children's Medical Center, Petah Tikva
| | - Orna Steinberg-Shemer
- The Rina Zaizov Division of Pediatric Hematology-Oncology, Schneider Children's Medical Center, Petah Tikva; Israel; Felsenstein Medical Research Center, Sackler School of Medicine Tel-Aviv University, Petah Tikva
| | - Qiu-Hua Huang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, Jiao Tong University School of Medicine, Shanghai 200025
| | - Yun Tan
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, Jiao Tong University School of Medicine, Shanghai 200025
| | - Sai-Juan Chen
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, Jiao Tong University School of Medicine, Shanghai 200025
| | - Shai Izraeli
- Department of Human Molecular Genetics and Biochemistry, Sackler Medical School, Aviv University, Aviv 69978, Israel; The Rina Zaizov Division of Pediatric Hematology-Oncology, Schneider Children's Medical Center, Petah Tikva; Israel; Functional Genomics and Childhood Leukaemia Research, Sheba Medical Centre, Tel-Hashomer, Israel; Felsenstein Medical Research Center, Sackler School of Medicine Tel-Aviv University, Petah Tikva.
| | - Yehudit Birger
- Department of Human Molecular Genetics and Biochemistry, Sackler Medical School, Aviv University, Aviv 69978, Israel; The Rina Zaizov Division of Pediatric Hematology-Oncology, Schneider Children's Medical Center, Petah Tikva; Israel; Functional Genomics and Childhood Leukaemia Research, Sheba Medical Centre, Tel-Hashomer, Israel; Felsenstein Medical Research Center, Sackler School of Medicine Tel-Aviv University, Petah Tikva.
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24
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Li Y, Deng K, Kaner J, Geyer JT, Ouseph M, Fang F, Xu K, Roboz G, Kluk MJ. Detection of Hybrid Fusion Transcripts, Aberrant Transcript Expression, and Specific Single Nucleotide Variants in Acute Leukemia and Myeloid Disorders with Recurrent Gene Rearrangements. Pathobiology 2023; 91:76-88. [PMID: 37490880 DOI: 10.1159/000532085] [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: 01/28/2023] [Accepted: 06/19/2023] [Indexed: 07/27/2023] Open
Abstract
INTRODUCTION A variety of gene rearrangements and molecular alterations are key drivers in the pathobiology of acute leukemia and myeloid disorders; current classification systems increasingly incorporate these findings in diagnostic algorithms. Therefore, clinical laboratories require versatile tools, which can detect an increasing number and variety of molecular and cytogenetic alterations of clinical significance. METHODS We validated an RNA-based next-generation sequencing (NGS) assay that enables the detection of: (i) numerous hybrid fusion transcripts (including rare/novel gene partners), (ii) aberrantly expressed EVI1 (MECOM) and IKZF1 (Del exons 4-7) transcripts, and (iii) hotspot variants in KIT, ABL1, NPM1 (relevant in the context of gene rearrangement status). RESULTS For hybrid fusion transcripts, the assay showed 98-100% concordance for known positive and negative samples, with an analytical sensitivity (i.e., limit of detection) of approximately 0.8% cells. Samples with underlying EVI1 (MECOM) translocations demonstrated increased EVI1 (MECOM) expression. Aberrant IKZF1 (Del exons 4-7) transcripts detectable with the assay were also present on orthogonal reverse transcription PCR. Specific hotspot mutations in KIT, ABL1, and NPM1 detected with the assay showed 100% concordance with orthogonal testing. Lastly, several illustrative samples are included to highlight the assay's clinically relevant contributions to patient workup. CONCLUSION Through its ability to simultaneously detect various gene rearrangements, aberrantly expressed transcripts, and hotspot mutations, this RNA-based NGS assay is a valuable tool for clinical laboratories to supplement other molecular and cytogenetic methods used in the diagnostic workup and in clinical research for patients with acute leukemia and myeloid disorders.
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Affiliation(s)
- Yuewei Li
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Kaifang Deng
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Justin Kaner
- Department of Medicine, Hematology and Medical Oncology, Clinical and Translational Leukemia Program, Weill Cornell Medicine, New York, New York, USA
| | - Julia T Geyer
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Madhu Ouseph
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Frank Fang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Kemin Xu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Gail Roboz
- Department of Medicine, Hematology and Medical Oncology, Clinical and Translational Leukemia Program, Weill Cornell Medicine, New York, New York, USA
| | - Michael J Kluk
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
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25
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Voit RA, Sankaran VG. MECOM Deficiency: from Bone Marrow Failure to Impaired B-Cell Development. J Clin Immunol 2023:10.1007/s10875-023-01545-0. [PMID: 37407873 DOI: 10.1007/s10875-023-01545-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/26/2023] [Indexed: 07/07/2023]
Abstract
MECOM deficiency is a recently identified inborn error of immunity and inherited bone marrow failure syndrome caused by haploinsufficiency of the hematopoietic transcription factor MECOM. It is unique among inherited bone marrow failure syndromes, many of which present during later childhood or adolescence, because of the early age of onset and severity of the pancytopenia, emphasizing the importance and gene dose dependency of MECOM during hematopoiesis. B-cell lymphopenia and hypogammaglobulinemia have been described in a subset of patients with MECOM deficiency. While the mechanisms underlying the B-cell deficiency are currently unknown, recent work has provided mechanistic insights into the function of MECOM in hematopoietic stem cell (HSC) maintenance. MECOM binds to regulatory enhancers that control the expression of a network of genes essential for HSC maintenance and self-renewal. Heterozygous mutations, as seen in MECOM-deficient bone marrow failure, lead to dysregulated MECOM network expression. Extra-hematopoietic manifestations of MECOM deficiency, including renal and cardiac anomalies, radioulnar synostosis, clinodactyly, and hearing loss, have been reported. Individuals with specific genotypes have some of the systemic manifestations with isolated mild thrombocytopenia or without hematologic abnormalities, highlighting the tissue specificity of mutations in some MECOM domains. Those infants with MECOM-associated bone marrow failure require HSC transplantation for survival. Here, we review the expanding cohort of patient phenotypes and accompanying genotypes resulting in MECOM deficiency, and the proposed mechanisms underlying MECOM regulation of human HSC maintenance and B-cell development.
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Affiliation(s)
- Richard A Voit
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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Zhao HG, Deininger M. Always stressed but never exhausted: how stem cells in myeloid neoplasms avoid extinction in inflammatory conditions. Blood 2023; 141:2797-2812. [PMID: 36947811 PMCID: PMC10315634 DOI: 10.1182/blood.2022017152] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/27/2023] [Accepted: 03/13/2023] [Indexed: 03/24/2023] Open
Abstract
Chronic or recurrent episodes of acute inflammation cause attrition of normal hematopoietic stem cells (HSCs) that can lead to hematopoietic failure but they drive progression in myeloid malignancies and their precursor clonal hematopoiesis. Mechanistic parallels exist between hematopoiesis in chronic inflammation and the continuously increased proliferation of myeloid malignancies, particularly myeloproliferative neoplasms (MPNs). The ability to enter dormancy, a state of deep quiescence characterized by low oxidative phosphorylation, low glycolysis, reduced protein synthesis, and increased autophagy is central to the preservation of long-term HSCs and likely MPN SCs. The metabolic features of dormancy resemble those of diapause, a state of arrested embryonic development triggered by adverse environmental conditions. To outcompete their normal counterparts in the inflammatory MPN environment, MPN SCs co-opt mechanisms used by HSCs to avoid exhaustion, including signal attenuation by negative regulators, insulation from activating cytokine signals, anti-inflammatory signaling, and epigenetic reprogramming. We propose that new therapeutic strategies may be derived from conceptualizing myeloid malignancies as an ecosystem out of balance, in which residual normal and malignant hematopoietic cells interact in multiple ways, only few of which have been characterized in detail. Disrupting MPN SC insulation to overcome dormancy, interfering with aberrant cytokine circuits that favor MPN cells, and directly boosting residual normal HSCs are potential strategies to tip the balance in favor of normal hematopoiesis. Although eradicating the malignant cell clones remains the goal of therapy, rebalancing the ecosystem may be a more attainable objective in the short term.
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Affiliation(s)
- Helong Gary Zhao
- Versiti Blood Research Institute and Medical College of Wisconsin, Milwaukee, WI
| | - Michael Deininger
- Versiti Blood Research Institute and Medical College of Wisconsin, Milwaukee, WI
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27
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Di Giorgio E, Benetti R, Kerschbamer E, Xodo L, Brancolini C. Super-enhancer landscape rewiring in cancer: The epigenetic control at distal sites. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 380:97-148. [PMID: 37657861 DOI: 10.1016/bs.ircmb.2023.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
Abstract
Super-enhancers evolve as elements at the top of the hierarchical control of gene expression. They are important end-gatherers of signaling pathways that control stemness, differentiation or adaptive responses. Many epigenetic regulations focus on these regions, and not surprisingly, during the process of tumorigenesis, various alterations can account for their dysfunction. Super-enhancers are emerging as key drivers of the aberrant gene expression landscape that sustain the aggressiveness of cancer cells. In this review, we will describe and discuss about the structure of super-enhancers, their epigenetic regulation, and the major changes affecting their functionality in cancer.
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Affiliation(s)
- Eros Di Giorgio
- Laboratory of Biochemistry, Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Roberta Benetti
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Emanuela Kerschbamer
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Luigi Xodo
- Laboratory of Biochemistry, Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Claudio Brancolini
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, Udine, Italy.
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28
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EVI1 drives leukemogenesis through aberrant ERG activation. Blood 2023; 141:453-466. [PMID: 36095844 DOI: 10.1182/blood.2022016592] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/10/2022] [Accepted: 08/28/2022] [Indexed: 02/07/2023] Open
Abstract
Chromosomal rearrangements involving the MDS1 and EVI1 complex locus (MECOM) on chromosome 3q26 define an aggressive subtype of acute myeloid leukemia (AML) that is associated with chemotherapy resistance and dismal prognosis. Established treatment regimens commonly fail in these patients, therefore, there is an urgent need for new therapeutic concepts that will require a better understanding of the molecular and cellular functions of the ecotropic viral integration site 1 (EVI1) oncogene. To characterize gene regulatory functions of EVI1 and associated dependencies in AML, we developed experimentally tractable human and murine disease models, investigated the transcriptional consequences of EVI1 withdrawal in vitro and in vivo, and performed the first genome-wide CRISPR screens in EVI1-dependent AML. By integrating conserved transcriptional targets with genetic dependency data, we identified and characterized the ETS transcription factor ERG as a direct transcriptional target of EVI1 that is aberrantly expressed and selectively required in both human and murine EVI1-driven AML. EVI1 controls the expression of ERG and occupies a conserved intragenic enhancer region in AML cell lines and samples from patients with primary AML. Suppression of ERG induces terminal differentiation of EVI1-driven AML cells, whereas ectopic expression of ERG abrogates their dependence on EVI1, indicating that the major oncogenic functions of EVI1 are mediated through aberrant transcriptional activation of ERG. Interfering with this regulatory axis may provide entry points for the development of rational targeted therapies.
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Tang Z, Wang W, Yang S, El Achi H, Fang H, Nahmod KA, Toruner GA, Xu J, Thakral B, Ayoub E, Issa GC, Yin CC, You MJ, Miranda RN, Khoury JD, Medeiros LJ, Tang G. 3q26.2/ MECOM Rearrangements by Pericentric Inv(3): Diagnostic Challenges and Clinicopathologic Features. Cancers (Basel) 2023; 15:458. [PMID: 36672407 PMCID: PMC9856433 DOI: 10.3390/cancers15020458] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
MECOM rearrangement (MECOM-R) resulting from 3q26.2 aberrations is often associated with myeloid neoplasms and inferior prognosis in affected patients. Uncommonly, certain 3q26.2/MECOM-R can be subtle/cryptic and consequently overlooked by karyotyping. We identified 17 acute myeloid leukemia (AML) patients (male/female: 13/4 with a median age of 67 years, range 42 to 85 years) with a pericentric inv(3) leading to MECOM-R, with breakpoints at 3p23 (n = 11), 3p25 (n = 3), 3p21 (n = 2) and 3p13 (n = 1) on 3p and 3q26.2 on 3q. These pericentric inv(3)s were overlooked by karyotyping initially in 16 of 17 cases and later detected by metaphase FISH analysis. Similar to the patients with classic/paracentric inv(3)(q21q26.2), patients with pericentric inv(3) exhibited frequent cytopenia, morphological dysplasia (especially megakaryocytes), -7/del(7q), frequent NRAS (n = 6), RUNX1 (n = 5) and FLT-3 (n = 4) mutations and dismal outcomes (median overall survival: 14 months). However, patients with pericentric inv(3) more frequently had AML with thrombocytopenia (n = 15, 88%), relative monocytosis in peripheral blood (n = 15, 88%), decreased megakaryocytes (n = 11, 65%), and lower SF3B1 mutation. We conclude that AML with pericentric inv(3) shares some similarities with AML associated with classic/paracentric inv(3)/GATA2::MECOM but also shows certain unique features. Pericentric inv(3)s are often subtle/cryptic by chromosomal analysis. A reflex FISH analysis for MECOM-R is recommended in myeloid neoplasms showing -7/del(7q).
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Affiliation(s)
- Zhenya Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wei Wang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Su Yang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hanadi El Achi
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hong Fang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Karen Amelia Nahmod
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gokce A. Toruner
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jie Xu
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Beenu Thakral
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Edward Ayoub
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ghayas C. Issa
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - C. Cameron Yin
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - M. James You
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Roberto N. Miranda
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Joseph D. Khoury
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - L. Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guilin Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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30
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Voit RA, Tao L, Yu F, Cato LD, Cohen B, Fleming TJ, Antoszewski M, Liao X, Fiorini C, Nandakumar SK, Wahlster L, Teichert K, Regev A, Sankaran VG. A genetic disorder reveals a hematopoietic stem cell regulatory network co-opted in leukemia. Nat Immunol 2023; 24:69-83. [PMID: 36522544 PMCID: PMC9810535 DOI: 10.1038/s41590-022-01370-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 10/25/2022] [Indexed: 12/23/2022]
Abstract
The molecular regulation of human hematopoietic stem cell (HSC) maintenance is therapeutically important, but limitations in experimental systems and interspecies variation have constrained our knowledge of this process. Here, we have studied a rare genetic disorder due to MECOM haploinsufficiency, characterized by an early-onset absence of HSCs in vivo. By generating a faithful model of this disorder in primary human HSCs and coupling functional studies with integrative single-cell genomic analyses, we uncover a key transcriptional network involving hundreds of genes that is required for HSC maintenance. Through our analyses, we nominate cooperating transcriptional regulators and identify how MECOM prevents the CTCF-dependent genome reorganization that occurs as HSCs differentiate. We show that this transcriptional network is co-opted in high-risk leukemias, thereby enabling these cancers to acquire stem cell properties. Collectively, we illuminate a regulatory network necessary for HSC self-renewal through the study of a rare experiment of nature.
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Affiliation(s)
- Richard A Voit
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Liming Tao
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Fulong Yu
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Liam D Cato
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Blake Cohen
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Travis J Fleming
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mateusz Antoszewski
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xiaotian Liao
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Claudia Fiorini
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Satish K Nandakumar
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Albert Einstein Cancer Center, Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Bronx, NY, USA
| | - Lara Wahlster
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kristian Teichert
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
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31
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Irie M, Niihori T, Nakano T, Suzuki T, Katayama S, Moriya K, Niizuma H, Suzuki N, Saito-Nanjo Y, Onuma M, Rikiishi T, Sato A, Hangai M, Hiwatari M, Ikeda J, Tanoshima R, Shiba N, Yuza Y, Yamamoto N, Hashii Y, Kato M, Takita J, Maeda M, Aoki Y, Imaizumi M, Sasahara Y. Reduced-intensity conditioning is effective for allogeneic hematopoietic stem cell transplantation in infants with MECOM-associated syndrome. Int J Hematol 2022; 117:598-606. [PMID: 36515795 PMCID: PMC10063491 DOI: 10.1007/s12185-022-03505-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/01/2022] [Accepted: 12/01/2022] [Indexed: 12/15/2022]
Abstract
Mutations in the MECOM encoding EVI1 are observed in infants who have radioulnar synostosis with amegakaryocytic thrombocytopenia. MECOM-associated syndrome was proposed based on clinical heterogeneity. Allogeneic hematopoietic stem cell transplantation (HSCT) is a curative treatment for progressive bone marrow failure. However, data regarding allogeneic HSCT for this rare disease are limited. We retrospectively assessed overall survival, conditioning regimen, regimen-related toxicities and long-term sequelae in six patients treated with allogeneic HSCT. All patients received a reduced-intensity conditioning (RIC) regimen consisting of fludarabine, cyclophosphamide or melphalan, and rabbit anti-thymocyte globulin and/or low-dose total body/thoracic-abdominal/total lymphoid irradiation, followed by allogeneic bone marrow or cord blood transplantation from unrelated donors between 4 and 18 months of age. All patients survived and achieved stable engraftment and complete chimerization with the donor type. Moreover, no patient experienced severe regimen-related toxicities, and only lower grades of acute graft-versus-host disease were observed. Three patients treated with low-dose irradiation had relatively short stature compared to three patients not treated with irradiation. Therefore, allogeneic HSCT with RIC is an effective and feasible treatment for infants with MECOM-associated syndrome. Future studies are needed to evaluate the use of low-dose irradiation to avoid risks of other long-term sequelae.
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Affiliation(s)
- Masahiro Irie
- Department of Pediatrics, Tohoku University Graduate School of Medicine, 1-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8574, Japan
| | - Tetsuya Niihori
- Department of Medical Genetics, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Tomohiro Nakano
- Department of Pediatrics, Tohoku University Graduate School of Medicine, 1-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8574, Japan
| | - Tasuku Suzuki
- Department of Pediatrics, Tohoku University Graduate School of Medicine, 1-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8574, Japan
| | - Saori Katayama
- Department of Pediatrics, Tohoku University Graduate School of Medicine, 1-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8574, Japan
| | - Kunihiko Moriya
- Department of Pediatrics, Tohoku University Graduate School of Medicine, 1-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8574, Japan
| | - Hidetaka Niizuma
- Department of Pediatrics, Tohoku University Graduate School of Medicine, 1-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8574, Japan
| | - Nobu Suzuki
- Department of Hematology and Oncology, Miyagi Children's Hospital, Miyagi, Japan
| | - Yuka Saito-Nanjo
- Department of Hematology and Oncology, Miyagi Children's Hospital, Miyagi, Japan
| | - Masaei Onuma
- Department of Hematology and Oncology, Miyagi Children's Hospital, Miyagi, Japan
| | - Takeshi Rikiishi
- Department of Hematology and Oncology, Miyagi Children's Hospital, Miyagi, Japan
| | - Atsushi Sato
- Department of Hematology and Oncology, Miyagi Children's Hospital, Miyagi, Japan
| | - Mayumi Hangai
- Department of Pediatrics, The University of Tokyo, Tokyo, Japan
| | - Mitsuteru Hiwatari
- Department of Pediatrics, The University of Tokyo, Tokyo, Japan.,Department of Pediatrics, School of Medicine, Teikyo University, Tokyo, Japan
| | - Junji Ikeda
- Department of Pediatrics, Yokohama City University Graduate School of Medicine, Kanagawa, Japan
| | - Reo Tanoshima
- Department of Pediatrics, Yokohama City University Graduate School of Medicine, Kanagawa, Japan
| | - Norio Shiba
- Department of Pediatrics, Yokohama City University Graduate School of Medicine, Kanagawa, Japan
| | - Yuki Yuza
- Department of Hematology and Oncology, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Nobuyuki Yamamoto
- Department of Pediatrics, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Yoshiko Hashii
- Department of Pediatrics, Osaka University Graduate School of Medicine, Osaka, Japan.,Department of Pediatrics, Osaka International Cancer Institute, Osaka, Japan
| | - Motohiro Kato
- Department of Pediatrics, The University of Tokyo, Tokyo, Japan.,Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Junko Takita
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Miho Maeda
- Department of Pediatrics, Nippon Medical School, Tokyo, Japan
| | - Yoko Aoki
- Department of Medical Genetics, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Masue Imaizumi
- Department of Hematology and Oncology, Miyagi Children's Hospital, Miyagi, Japan
| | - Yoji Sasahara
- Department of Pediatrics, Tohoku University Graduate School of Medicine, 1-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8574, Japan.
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32
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Therapy Resistance and Disease Progression in CML: Mechanistic Links and Therapeutic Strategies. Curr Hematol Malig Rep 2022; 17:181-197. [PMID: 36258106 DOI: 10.1007/s11899-022-00679-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2022] [Indexed: 01/27/2023]
Abstract
PURPOSE OF REVIEW Despite the adoption of tyrosine kinases inhibitors (TKIs) as molecular targeted therapy in chronic myeloid leukemia, some patients do not respond to treatment and even experience disease progression. This review aims to give a broad summary of advances in understanding of the mechanisms of therapy resistance, as well as management strategies that may overcome or prevent the emergence of drug resistance. Ultimately, the goal of therapy is the cure of CML, which will also require an increased understanding of the leukemia stem cell (LSC). RECENT FINDINGS Resistance to tyrosine kinase inhibitors stems from a range of possible causes. Mutations of the BCR-ABL1 fusion oncoprotein have been well-studied. Other causes range from cell-intrinsic factors, such as the inherent resistance of primitive stem cells to drug treatment, to mechanisms extrinsic to the leukemic compartment that help CML cells evade apoptosis. There exists heterogeneity in TKI response among different hematopoietic populations in CML. The abundances of these TKI-sensitive and TKI-insensitive populations differ from patient to patient and contribute to response heterogeneity. It is becoming clear that targeting the BCR-ABL1 kinase through TKIs is only one part of the equation, and TKI usage alone may not cure the majority of patients with CML. Considerable effort should be devoted to targeting the BCR-ABL1-independent mechanisms of resistance and persistence of CML LSCs.
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33
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EVI1 expression in early-stage breast cancer patients treated with neoadjuvant chemotherapy. BMC Cancer 2022; 22:1040. [PMID: 36195836 PMCID: PMC9533588 DOI: 10.1186/s12885-022-10109-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/16/2022] [Indexed: 11/10/2022] Open
Abstract
Background Overexpression of the EVI1 (ecotropic viral integration site 1) oncogene has recently been implicated as a prognostic factor in breast cancer (BC), particularly in triple-negative BC (TNBC). In this study we aimed to investigate frequency and clinical relevance of EVI1 expression in newly diagnosed BC treated with neoadjuvant chemotherapy. Methods EVI1 expression was determined by immunohistochemistry using H-score as a cumulative measurement of protein expression in pretherapeutic biopsies of BC patients treated with anthracycline/taxane based neoadjuvant chemotherapy within the GeparTrio trial. EVI1 was analyzed as a continuous variable and dichotomized into low or high based on median expression. Endpoints were pathological complete response (pCR), disease-free survival (DFS) and overall survival (OS). Results Of the 993 tumors analyzed, 882 had available subtype information: 50.8% were HR + /HER2-, 15% HR + /HER2 + , 9.8% HR-/HER2 + , and 24.5% TNBC. Median EVI1 H-score was 112.16 (range 0.5–291.4). High EVI1 expression was significantly associated with smaller tumor size (p = 0.002) but not with BC subtype. Elevated EVI1 levels were not significantly associated with therapy response and survival in the entire cohort or within BC subtypes. However, TNBC patients with high EVI1 showed a trend towards increased pCR rates compared to low group (37.7% vs 27.5%, p = 0.114; odds ratio 1.60 (95%CI 0.90–2.85, p = 0.110) and numerically better DFS (HR = 0.77 [95%CI 0.48–1.23], log-rank p = 0.271) and OS (HR = 0.76 [95% 0.44–1.31], log-rank p = 0.314) without reaching statistical significance. Conclusion EVI1 was not associated with response to neoadjuvant therapy or patient survival in the overall cohort. Further analyses are needed to verify our findings especially in the pathological work-up of early-stage HER2-negative BC patients. Trial registration NCT00544765. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-10109-1.
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34
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Mutant SF3B1 splices a more leukemogenic EVI1. Blood 2022; 140:800-801. [PMID: 36006671 DOI: 10.1182/blood.2022017380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 06/17/2022] [Indexed: 11/20/2022] Open
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35
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Tanaka A, Nakano TA, Nomura M, Yamazaki H, Bewersdorf JP, Mulet-Lazaro R, Hogg S, Liu B, Penson A, Yokoyama A, Zang W, Havermans M, Koizumi M, Hayashi Y, Cho H, Kanai A, Lee SC, Xiao M, Koike Y, Zhang Y, Fukumoto M, Aoyama Y, Konuma T, Kunimoto H, Inaba T, Nakajima H, Honda H, Kawamoto H, Delwel R, Abdel-Wahab O, Inoue D. Aberrant EVI1 splicing contributes to EVI1-rearranged leukemia. Blood 2022; 140:875-888. [PMID: 35709354 PMCID: PMC9412007 DOI: 10.1182/blood.2021015325] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 06/06/2022] [Indexed: 11/20/2022] Open
Abstract
Detailed genomic and epigenomic analyses of MECOM (the MDS1 and EVI1 complex locus) have revealed that inversion or translocation of chromosome 3 drives inv(3)/t(3;3) myeloid leukemias via structural rearrangement of an enhancer that upregulates transcription of EVI1. Here, we identify a novel, previously unannotated oncogenic RNA-splicing derived isoform of EVI1 that is frequently present in inv(3)/t(3;3) acute myeloid leukemia (AML) and directly contributes to leukemic transformation. This EVI1 isoform is generated by oncogenic mutations in the core RNA splicing factor SF3B1, which is mutated in >30% of inv(3)/t(3;3) myeloid neoplasm patients and thereby represents the single most commonly cooccurring genomic alteration in inv(3)/t(3;3) patients. SF3B1 mutations are statistically uniquely enriched in inv(3)/t(3;3) myeloid neoplasm patients and patient-derived cell lines compared with other forms of AML and promote mis-splicing of EVI1 generating an in-frame insertion of 6 amino acids at the 3' end of the second zinc finger domain of EVI1. Expression of this EVI1 splice variant enhanced the self-renewal of hematopoietic stem cells, and introduction of mutant SF3B1 in mice bearing the humanized inv(3)(q21q26) allele resulted in generation of this novel EVI1 isoform in mice and hastened leukemogenesis in vivo. The mutant SF3B1 spliceosome depends upon an exonic splicing enhancer within EVI1 exon 13 to promote usage of a cryptic branch point and aberrant 3' splice site within intron 12 resulting in the generation of this isoform. These data provide a mechanistic basis for the frequent cooccurrence of SF3B1 mutations as well as new insights into the pathogenesis of myeloid leukemias harboring inv(3)/t(3;3).
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Affiliation(s)
- Atsushi Tanaka
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Laboratory of Immunology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Taizo A Nakano
- Department of Pediatrics, Section of Hematology, Oncology and Bone Marrow Transplantation, University of Colorado, Aurora, CO
| | - Masaki Nomura
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Facility for iPS Cell Therapy, CiRA Foundation, Kyoto, Japan
| | - Hiromi Yamazaki
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Jan P Bewersdorf
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Roger Mulet-Lazaro
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Simon Hogg
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Bo Liu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Alex Penson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Akihiko Yokoyama
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Yamagata, Japan
| | - Weijia Zang
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Marije Havermans
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Miho Koizumi
- Field of Human Disease Models, Major in Advanced Life Sciences and Medicine, Tokyo Women's Medical University, Tokyo, Japan
| | - Yasutaka Hayashi
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Hana Cho
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Akinori Kanai
- Department of Molecular Oncology and Leukemia Program Project, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Stanley C Lee
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Muran Xiao
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yui Koike
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Yifan Zhang
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Miki Fukumoto
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Yumi Aoyama
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | - Hiroyoshi Kunimoto
- Department of Stem Cell and Immune Regulation, Graduate School of Medicine, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Toshiya Inaba
- Department of Molecular Oncology and Leukemia Program Project, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Hideaki Nakajima
- Department of Stem Cell and Immune Regulation, Graduate School of Medicine, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Hiroaki Honda
- Field of Human Disease Models, Major in Advanced Life Sciences and Medicine, Tokyo Women's Medical University, Tokyo, Japan
| | - Hiroshi Kawamoto
- Laboratory of Immunology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Ruud Delwel
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Daichi Inoue
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
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Enhancer retargeting of CDX2 and UBTF::ATXN7L3 define a subtype of high-risk B-progenitor acute lymphoblastic leukemia. Blood 2022; 139:3519-3531. [PMID: 35192684 PMCID: PMC9203703 DOI: 10.1182/blood.2022015444] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/12/2022] [Indexed: 01/14/2023] Open
Abstract
Transcriptome sequencing has identified multiple subtypes of B-progenitor acute lymphoblastic leukemia (B-ALL) of prognostic significance, but a minority of cases lack a known genetic driver. Here, we used integrated whole-genome (WGS) and -transcriptome sequencing (RNA-seq), enhancer mapping, and chromatin topology analysis to identify previously unrecognized genomic drivers in B-ALL. Newly diagnosed (n = 3221) and relapsed (n = 177) B-ALL cases with tumor RNA-seq were studied. WGS was performed to detect mutations, structural variants, and copy number alterations. Integrated analysis of histone 3 lysine 27 acetylation and chromatin looping was performed using HiChIP. We identified a subset of 17 newly diagnosed and 5 relapsed B-ALL cases with a distinct gene expression profile and 2 universal and unique genomic alterations resulting from aberrant recombination-activating gene activation: a focal deletion downstream of PAN3 at 13q12.2 resulting in CDX2 deregulation by the PAN3 enhancer and a focal deletion of exons 18-21 of UBTF at 17q21.31 resulting in a chimeric fusion, UBTF::ATXN7L3. A subset of cases also had rearrangement and increased expression of the PAX5 gene, which is otherwise uncommon in B-ALL. Patients were more commonly female and young adult with median age 35 (range,12-70 years). The immunophenotype was characterized by CD10 negativity and immunoglobulin M positivity. Among 16 patients with known clinical response, 9 (56.3%) had high-risk features including relapse (n = 4) or minimal residual disease >1% at the end of remission induction (n = 5). CDX2-deregulated, UBTF::ATXN7L3 rearranged (CDX2/UBTF) B-ALL is a high-risk subtype of leukemia in young adults for which novel therapeutic approaches are required.
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Shi Q, Zhang B, Bsirini C, Li L, Giampoli EJ, Magliocca KR, Reid M, Zhou Z. NR4A3 Fluorescence In Situ Hybridization Analysis in Cytologic and Surgical Specimens of acinic cell carcinoma. Hum Pathol 2022; 127:86-91. [PMID: 35700750 DOI: 10.1016/j.humpath.2022.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 05/17/2022] [Accepted: 06/07/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Acinic cell carcinoma (AciCC) may pose a diagnostic challenge, particularly on small biopsies and fine needle aspiration (FNA) because of its variable histology including potential high grade transformation and its mimickers. Immunoreactivity with circumferential membranous staining for DOG1 can support the diagnosis of AciCC but is not entirely specific. A novel rearrangement t(4;9)(q13;q31) leading to upregulation of nuclear receptor subfamily 4 group A member 3 (NR4A3) has been described in AciCC, is potentially detectable by Fluorescence in situ hybridization (FISH) and may be useful in the evaluation for AciCC. METHODS Using NR4A3 Dual Color Break Apart Probe (Zytovision, Germany) FISH was performed on AciCCs from three large academic institutions. NR4A3 rearrangement was defined as positive signal patterns in 15% of tissue interphase nuclei. RESULTS 52 AciCCs including 47 resections and 5 FNAs (including 5 paired FNA/resections) were analyzed. 5 non-AciCC salivary gland tumors and 2 sialadenitis cases were used as controls. 8 (15%) (8/52) AciCCs failed FISH testing. FISH was positive in 23 AciCCs (sensitivity 59%, 23/39) with 100% concordance between five matched resection/FNAs (three were positive for FISH and two were negative). FISH was negative in all non-AciCCs (specificity: 100%, 0/7). CONCLUSION NR4A3 FISH has a sensitivity of 59% and specificity of 100% in detecting AciCC which suggests that NR4A3 rearrangement-driven upregulation is a recurrent, specific oncogenic event in AciCC, consistent with prior results. 100% concordance between matched FNA/resection samples validate its potential utility on cytology samples.
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Affiliation(s)
- Qiuying Shi
- Department of Pathology and Laboratory Medicine, Emory University Hospital, Atlanta GA 30308, USA
| | - Bin Zhang
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, 601 Elmwood Avenue, Box 626, Rochester, NY 14642, USA
| | - Caroline Bsirini
- Department of Pathology and Laboratory Medicine, Emory University Hospital, Atlanta GA 30308, USA
| | - Liqiong Li
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, 601 Elmwood Avenue, Box 626, Rochester, NY 14642, USA
| | - Ellen J Giampoli
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, 601 Elmwood Avenue, Box 626, Rochester, NY 14642, USA
| | - Kelly R Magliocca
- Department of Pathology and Laboratory Medicine, Emory University Hospital, Atlanta GA 30308, USA
| | - Michelle Reid
- Department of Pathology and Laboratory Medicine, Emory University Hospital, Atlanta GA 30308, USA
| | - Zhongren Zhou
- Department of Pathology, Robert Wood Johnson Medical School and New Jersey Medical School, Rutgers University, New Brunswick, NJ 08901, USA.
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Yoshino S, Suzuki HI. The molecular understanding of super-enhancer dysregulation in cancer. NAGOYA JOURNAL OF MEDICAL SCIENCE 2022; 84:216-229. [PMID: 35967935 PMCID: PMC9350580 DOI: 10.18999/nagjms.84.2.216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/20/2022] [Indexed: 11/30/2022]
Abstract
Abnormalities in the regulation of gene expression are associated with various pathological conditions. Among the distal regulatory elements in the genome, the activation of target genes by enhancers plays a central role in the formation of cell type-specific gene expression patterns. Super-enhancers are a subclass of enhancers that frequently contain multiple enhancer-like elements and are characterized by dense binding of master transcription factors and Mediator complexes and high signals of active histone marks. Super-enhancers have been studied in detail as important regulatory regions that control cell identity and contribute to the pathogenesis of diverse diseases. In cancer, super-enhancers have multifaceted roles by activating various oncogenes and other cancer-related genes and shaping characteristic gene expression patterns in cancer cells. Alterations in super-enhancer activities in cancer involve multiple mechanisms, including the dysregulation of transcription factors and the super-enhancer-associated genomic abnormalities. The study of super-enhancers could contribute to the identification of effective biomarkers and the development of cancer therapeutics targeting transcriptional addiction. In this review, we summarize the roles of super-enhancers in cancer biology, with a particular focus on hematopoietic malignancies, in which multiple super-enhancer alteration mechanisms have been reported.
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Affiliation(s)
- Seiko Yoshino
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.
| | - Hiroshi I. Suzuki
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.
,Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan
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Johnson KD, Soukup AA, Bresnick EH. GATA2 deficiency elevates interferon regulatory factor-8 to subvert a progenitor cell differentiation program. Blood Adv 2022; 6:1464-1473. [PMID: 35008108 PMCID: PMC8905696 DOI: 10.1182/bloodadvances.2021006182] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/17/2021] [Indexed: 11/20/2022] Open
Abstract
Cell type-specific transcription factors control stem and progenitor cell transitions by establishing networks containing hundreds of genes and proteins. Network complexity renders it challenging to discover essential versus modulatory or redundant components. This scenario is exemplified by GATA2 regulation of hematopoiesis during embryogenesis. Loss of a far upstream Gata2 enhancer (-77) disrupts the GATA2-dependent transcriptome governing hematopoietic progenitor cell differentiation. The aberrant transcriptome includes the transcription factor interferon regulatory factor 8 (IRF8) and a host of innate immune regulators. Mutant progenitors lose the capacity to balance production of diverse hematopoietic progeny. To elucidate mechanisms, we asked if IRF8 is essential, contributory, or not required. Reducing Irf8, in the context of the -77 mutant allele, reversed granulocytic deficiencies and the excessive accumulation of dendritic cell committed progenitors. Despite many dysregulated components that control vital transcriptional, signaling, and immune processes, the aberrant elevation of a single transcription factor deconstructed the differentiation program.
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Affiliation(s)
| | - Alexandra A. Soukup
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Emery H. Bresnick
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI
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40
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Role of Biomarkers in FLT3 AML. Cancers (Basel) 2022; 14:cancers14051164. [PMID: 35267471 PMCID: PMC8909069 DOI: 10.3390/cancers14051164] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 12/19/2022] Open
Abstract
Simple Summary Genetically heterogeneous disorder acute myeloid leukemia (AML) is marked by recurring mutations in FLT3. Current FLT3 inhibitors and other emerging inhibitors have helped in the improvement of the quality of standard of care therapies; however, the overall survival of the patients remains static. This is due to numerous mutations in FLT3, which causes resistance against these FLT3 inhibitors. For effective treatment of AML patients, alternative approaches are required to overcome this resistance. Here, we will summarize the biomarkers for FLT3 inhibitors in AML, as well as the alternative measures to overcome resistance to the current therapies. Abstract Acute myeloid leukemia is a disease characterized by uncontrolled proliferation of clonal myeloid blast cells that are incapable of maturation to leukocytes. AML is the most common leukemia in adults and remains a highly fatal disease with a five-year survival rate of 24%. More than 50% of AML patients have mutations in the FLT3 gene, rendering FLT3 an attractive target for small-molecule inhibition. Currently, there are several FLT3 inhibitors in the clinic, and others remain in clinical trials. However, these inhibitors face challenges due to lack of efficacy against several FLT3 mutants. Therefore, the identification of biomarkers is vital to stratify AML patients and target AML patient population with a particular FLT3 mutation. Additionally, there is an unmet need to identify alternative approaches to combat the resistance to FLT3 inhibitors. Here, we summarize the current knowledge on the utilization of diagnostic, prognostic, predictive, and pharmacodynamic biomarkers for FLT3-mutated AML. The resistance mechanisms to various FLT3 inhibitors and alternative approaches to combat this resistance are also discussed and presented.
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Gao J, Gurbuxani S, Zak T, Kocherginsky M, Ji P, Wehbe F, Chen Q, Chen YH, Lu X, Jennings L, Frankfurt O, Altman J, Sukhanova M. Comparison of myeloid neoplasms with nonclassic 3q26.2/MECOM versus classic inv(3)/t(3;3) rearrangements reveals diverse clinicopathologic features, genetic profiles, and molecular mechanisms of MECOM activation. Genes Chromosomes Cancer 2022; 61:71-80. [PMID: 34668265 DOI: 10.1002/gcc.23004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 11/05/2022] Open
Abstract
MECOM rearrangements are recurrent in myeloid neoplasms and associated with poor prognosis. However, only inv(3)(q21q26.2) and t(3;3)(q21;q26.2), the classic MECOM rearrangements resulting in RPN1-MECOM rearrangement with Mecom overexpression and GATA2 haploinsufficiency, define the distinct subtype of acute myeloid leukemia (AML), and serve as presumptive evidence for myelodysplastic syndrome based on the current World Health Organization classification. Myeloid neoplasms with nonclassic 3q26.2/MECOM rearrangements have been found to be clinically aggressive, but comparative analysis of clinicopathologic and genomic features is limited. We retrospectively studied cohorts of myeloid neoplasms with classic and nonclassic MECOM rearrangements. Cases with classic rearrangements consisted predominantly of AML, often with inv(3) or t(3;3) as the sole chromosome abnormality, whereas the group of nonclassic rearrangements included a variety of myeloid neoplasms, often with complex karyotype without TP53 mutations and similarly dismal overall survival. Immunohistochemistry revealed Mecom protein overexpression in both groups, but overexpression in cases with nonclassic rearrangements was mediated through a mechanism other than GATA2 distal enhancer involvement typical for classic rearrangement. Our results demonstrated that myeloid neoplasms with nonclassic 3q26.2/MECOM rearrangements encompass a diverse group of diseases with poor clinical outcome, overexpression of Mecom protein as a result of the nonclassic mechanism of MECOM activation.
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Affiliation(s)
- Juehua Gao
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Sandeep Gurbuxani
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
| | - Taylor Zak
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Masha Kocherginsky
- Department of Preventive Medicine (Health and Biomedical Informatics), Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Peng Ji
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Firas Wehbe
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Department of Preventive Medicine (Health and Biomedical Informatics), Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Qing Chen
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Yi-Hua Chen
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Xinyan Lu
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Lawrence Jennings
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Olga Frankfurt
- Department of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Jessica Altman
- Department of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Madina Sukhanova
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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Kerbs P, Vosberg S, Krebs S, Graf A, Blum H, Swoboda A, Batcha AMN, Mansmann U, Metzler D, Heckman CA, Herold T, Greif PA. Fusion gene detection by RNA-sequencing complements diagnostics of acute myeloid leukemia and identifies recurring NRIP1-MIR99AHG rearrangements. Haematologica 2022; 107:100-111. [PMID: 34134471 PMCID: PMC8719081 DOI: 10.3324/haematol.2021.278436] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/03/2021] [Indexed: 12/04/2022] Open
Abstract
Identification of fusion genes in clinical routine is mostly based on cytogenetics and targeted molecular genetics, such as metaphase karyotyping, fluorescence in situ hybridization and reverse-transcriptase polymerase chain reaction. However, sequencing technologies are becoming more important in clinical routine as processing time and costs per sample decrease. To evaluate the performance of fusion gene detection by RNAsequencing compared to standard diagnostic techniques, we analyzed 806 RNA-sequencing samples from patients with acute myeloid leukemia using two state-of-the-art software tools, namely Arriba and FusionCatcher. RNA-sequencing detected 90% of fusion events that were reported by routine with high evidence, while samples in which RNA-sequencing failed to detect fusion genes had overall lower and inhomogeneous sequence coverage. Based on properties of known and unknown fusion events, we developed a workflow with integrated filtering strategies for the identification of robust fusion gene candidates by RNA-sequencing. Thereby, we detected known recurrent fusion events in 26 cases that were not reported by routine and found discrepancies in evidence for known fusion events between routine and RNA-sequencing in three cases. Moreover, we identified 157 fusion genes as novel robust candidates and comparison to entries from ChimerDB or Mitelman Database showed novel recurrence of fusion genes in 14 cases. Finally, we detected the novel recurrent fusion gene NRIP1- MIR99AHG resulting from inv(21)(q11.2;q21.1) in nine patients (1.1%) and LTN1-MX1 resulting from inv(21)(q21.3;q22.3) in two patients (0.25%). We demonstrated that NRIP1-MIR99AHG results in overexpression of the 3' region of MIR99AHG and the disruption of the tricistronic miRNA cluster miR-99a/let-7c/miR-125b-2. Interestingly, upregulation of MIR99AHG and deregulation of the miRNA cluster, residing in the MIR99AHG locus, are known mechanisms of leukemogenesis in acute megakaryoblastic leukemia. Our findings demonstrate that RNA-sequencing has a strong potential to improve the systematic detection of fusion genes in clinical applications and provides a valuable tool for fusion discovery.
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Affiliation(s)
- Paul Kerbs
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany; German Cancer Consortium (DKTK), partner site Munich; and; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian Vosberg
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany; German Cancer Consortium (DKTK), partner site Munich; and; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Anja Swoboda
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Aarif M N Batcha
- Department of Medical Data Processing, Biometry and Epidemiology, LMU Munich, Munich, Germany
| | - Ulrich Mansmann
- Department of Medical Data Processing, Biometry and Epidemiology, LMU Munich, Munich, Germany
| | - Dirk Metzler
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Caroline A Heckman
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Tobias Herold
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany; German Cancer Consortium (DKTK), partner site Munich; and; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp A Greif
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany; German Cancer Consortium (DKTK), partner site Munich; and; German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Montefiori LE, Mullighan CG. Redefining the biological basis of lineage-ambiguous leukemia through genomics: BCL11B deregulation in acute leukemias of ambiguous lineage. Best Pract Res Clin Haematol 2021; 34:101329. [PMID: 34865701 DOI: 10.1016/j.beha.2021.101329] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Acute leukemias of ambiguous lineage (ALAL), including mixed phenotype acute leukemia (MPAL) and related entities such as early T-cell precursor acute leukemia (ETP-ALL), remain diagnostic and clinical challenges due to limited understanding of pathogenesis, reliance of immunophenotyping to classify disease, and the lack of a rational approach to guide selection of appropriate therapy. Recent studies utilizing genomic sequencing and complementary approaches have provided key insights that are changing the way in which such leukemias are classified, and potentially, treated. Several recurrent genomic alterations define leukemias that straddle immunophenotypic entities, such as ZNF384-rearranged childhood B-ALL and B/myeloid MPAL, and BCL11B-rearranged T/myeloid MPAL, ETP-ALL and AML. In contrast, some cases of MPAL represent canonical ALL/AML entities exhibiting lineage aberrancy. For many cases of ALAL, experimental approaches indicate lineage aberrancy arises from acquisition of a founding genetic alteration into a hematopoietic stem or progenitor cell. Determination of optimal therapeutic approach requires genomic characterization of uniformly treated ALAL patients in prospective studies, but several approaches, including kinase inhibitors and BH3 mimetics may be efficacious in subsets of ALAL.
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Affiliation(s)
- Lindsey E Montefiori
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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44
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Grasedieck S, Cabantog A, MacPhee L, Im J, Ruess C, Demir B, Sperb N, Rücker FG, Döhner K, Herold T, Pollack JR, Bullinger L, Rouhi A, Kuchenbauer F. The retinoic acid receptor co-factor NRIP1 is uniquely upregulated and represents a therapeutic target in acute myeloid leukemia with chromosome 3q rearrangements. Haematologica 2021; 107. [PMID: 34854277 PMCID: PMC9335095 DOI: 10.3324/haematol.2020.276048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Aberrant expression of Ecotropic Viral Integration Site 1 (EVI1) is a hallmark of acute myeloid leukemia (AML) with inv(3) or t(3;3), which is a disease subtype with especially poor outcome. In studying transcriptomes from AML patients with chromosome 3q rearrangements, we identified a significant upregulation of the Nuclear Receptor Interacting Protein 1 (NRIP1) as well as its adjacent non-coding RNA LOC101927745. Utilizing transcriptomic and epigenomic data from over 900 primary samples from patients as well as genetic and transcriptional engineering approaches, we have identified several mechanisms that can lead to upregulation of NRIP1 in AML. We hypothesize that the LOC101927745 transcription start site harbors a context-dependent enhancer that is bound by EVI1, causing upregulation of NRIP1 in AML with chromosome 3 abnormalities. Furthermore, we showed that NRIP1 knockdown negatively affects the proliferation and survival of 3qrearranged AML cells and increases their sensitivity to all-trans retinoic acid, suggesting that NRIP1 is relevant for the pathogenesis of inv(3)/t(3;3) AML and could serve as a novel therapeutic target in myeloid malignancies with 3q abnormalities.
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Affiliation(s)
- Sarah Grasedieck
- University of British Columbia, Department of Microbiology & Immunology, Vancouver, British Columbia, Canada
| | - Ariene Cabantog
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Liam MacPhee
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Junbum Im
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Christoph Ruess
- Ulm University Hospital, Department of Internal Medicine III, Ulm, Germany
| | - Burcu Demir
- Ulm University Hospital, Department of Internal Medicine III, Ulm, Germany
| | - Nadine Sperb
- Ulm University Hospital, Department of Internal Medicine III, Ulm, Germany
| | - Frank G. Rücker
- Ulm University Hospital, Department of Internal Medicine III, Ulm, Germany
| | - Konstanze Döhner
- Ulm University Hospital, Department of Internal Medicine III, Ulm, Germany
| | - Tobias Herold
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Jonathan R. Pollack
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lars Bullinger
- Department of Hematology, Oncology and Tumor Immunology, Charité University Medicine, Berlin, Germany
| | - Arefeh Rouhi
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada,AR and FK contributed equally as co-senior authors
| | - Florian Kuchenbauer
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada,AR and FK contributed equally as co-senior authors
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45
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Thoms JAI, Truong P, Subramanian S, Knezevic K, Harvey G, Huang Y, Seneviratne JA, Carter DR, Joshi S, Skhinas J, Chacon D, Shah A, de Jong I, Beck D, Göttgens B, Larsson J, Wong JWH, Zanini F, Pimanda JE. Disruption of a GATA2-TAL1-ERG regulatory circuit promotes erythroid transition in healthy and leukemic stem cells. Blood 2021; 138:1441-1455. [PMID: 34075404 DOI: 10.1182/blood.2020009707] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 05/03/2021] [Indexed: 10/21/2022] Open
Abstract
Changes in gene regulation and expression govern orderly transitions from hematopoietic stem cells to terminally differentiated blood cell types. These transitions are disrupted during leukemic transformation, but knowledge of the gene regulatory changes underpinning this process is elusive. We hypothesized that identifying core gene regulatory networks in healthy hematopoietic and leukemic cells could provide insights into network alterations that perturb cell state transitions. A heptad of transcription factors (LYL1, TAL1, LMO2, FLI1, ERG, GATA2, and RUNX1) bind key hematopoietic genes in human CD34+ hematopoietic stem and progenitor cells (HSPCs) and have prognostic significance in acute myeloid leukemia (AML). These factors also form a densely interconnected circuit by binding combinatorially at their own, and each other's, regulatory elements. However, their mutual regulation during normal hematopoiesis and in AML cells, and how perturbation of their expression levels influences cell fate decisions remains unclear. In this study, we integrated bulk and single-cell data and found that the fully connected heptad circuit identified in healthy HSPCs persists, with only minor alterations in AML, and that chromatin accessibility at key heptad regulatory elements was predictive of cell identity in both healthy progenitors and leukemic cells. The heptad factors GATA2, TAL1, and ERG formed an integrated subcircuit that regulates stem cell-to-erythroid transition in both healthy and leukemic cells. Components of this triad could be manipulated to facilitate erythroid transition providing a proof of concept that such regulatory circuits can be harnessed to promote specific cell-type transitions and overcome dysregulated hematopoiesis.
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Affiliation(s)
| | - Peter Truong
- Adult Cancer Program, and
- Prince of Wales Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia
| | - Shruthi Subramanian
- Adult Cancer Program, and
- Prince of Wales Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia
| | - Kathy Knezevic
- Adult Cancer Program, and
- Prince of Wales Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia
| | - Gregory Harvey
- Adult Cancer Program, and
- Prince of Wales Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia
| | - Yizhou Huang
- Adult Cancer Program, and
- Prince of Wales Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW, Australia
| | - Janith A Seneviratne
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Daniel R Carter
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW, Australia
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Swapna Joshi
- Adult Cancer Program, and
- Prince of Wales Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia
| | - Joanna Skhinas
- Adult Cancer Program, and
- Prince of Wales Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia
| | - Diego Chacon
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW, Australia
| | - Anushi Shah
- Adult Cancer Program, and
- Prince of Wales Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia
| | - Ineke de Jong
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Dominik Beck
- Adult Cancer Program, and
- Prince of Wales Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW, Australia
| | - Berthold Göttgens
- Wellcome and Medical Research Council (MRC) Cambridge Stem Cell Institute, Cambridge, United Kingdom
| | - Jonas Larsson
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Jason W H Wong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Fabio Zanini
- Adult Cancer Program, and
- Prince of Wales Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia; and
| | - John E Pimanda
- School of Medical Sciences
- Adult Cancer Program, and
- Prince of Wales Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia
- Department of Haematology, Prince of Wales Hospital, Randwick, NSW, Australia
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46
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Maurya SS. Role of Enhancers in Development and Diseases. EPIGENOMES 2021; 5:epigenomes5040021. [PMID: 34968246 PMCID: PMC8715447 DOI: 10.3390/epigenomes5040021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/21/2021] [Accepted: 09/28/2021] [Indexed: 12/26/2022] Open
Abstract
Enhancers are cis-regulatory elements containing short DNA sequences that serve as binding sites for pioneer/regulatory transcription factors, thus orchestrating the regulation of genes critical for lineage determination. The activity of enhancer elements is believed to be determined by transcription factor binding, thus determining the cell state identity during development. Precise spatio-temporal control of the transcriptome during lineage specification requires the coordinated binding of lineage-specific transcription factors to enhancers. Thus, enhancers are the primary determinants of cell identity. Numerous studies have explored the role and mechanism of enhancers during development and disease, and various basic questions related to the functions and mechanisms of enhancers have not yet been fully answered. In this review, we discuss the recently published literature regarding the roles of enhancers, which are critical for various biological processes governing development. Furthermore, we also highlight that altered enhancer landscapes provide an essential context to understand the etiologies and mechanisms behind numerous complex human diseases, providing new avenues for effective enhancer-based therapeutic interventions.
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Affiliation(s)
- Shailendra S Maurya
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Department of Developmental Biology, School of Medicine, Washington University in St. Louis, 660 South Euclid Avenue, St. Louis, MO 63110, USA
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47
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Yun H, Narayan N, Vohra S, Giotopoulos G, Mupo A, Madrigal P, Sasca D, Lara-Astiaso D, Horton SJ, Agrawal-Singh S, Meduri E, Basheer F, Marando L, Gozdecka M, Dovey OM, Castillo-Venzor A, Wang X, Gallipoli P, Müller-Tidow C, Osborne CS, Vassiliou GS, Huntly BJP. Mutational synergy during leukemia induction remodels chromatin accessibility, histone modifications and three-dimensional DNA topology to alter gene expression. Nat Genet 2021; 53:1443-1455. [PMID: 34556857 PMCID: PMC7611829 DOI: 10.1038/s41588-021-00925-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 07/28/2021] [Indexed: 02/08/2023]
Abstract
Altered transcription is a cardinal feature of acute myeloid leukemia (AML); however, exactly how mutations synergize to remodel the epigenetic landscape and rewire three-dimensional DNA topology is unknown. Here, we apply an integrated genomic approach to a murine allelic series that models the two most common mutations in AML: Flt3-ITD and Npm1c. We then deconvolute the contribution of each mutation to alterations of the epigenetic landscape and genome organization, and infer how mutations synergize in the induction of AML. Our studies demonstrate that Flt3-ITD signals to chromatin to alter the epigenetic environment and synergizes with mutations in Npm1c to alter gene expression and drive leukemia induction. These analyses also allow the identification of long-range cis-regulatory circuits, including a previously unknown superenhancer of Hoxa locus, as well as larger and more detailed gene-regulatory networks, driven by transcription factors including PU.1 and IRF8, whose importance we demonstrate through perturbation of network members.
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MESH Headings
- Animals
- Base Sequence
- Chromatin Assembly and Disassembly/genetics
- DNA, Neoplasm/chemistry
- Disease Models, Animal
- Enhancer Elements, Genetic/genetics
- Gene Expression Regulation, Leukemic
- Gene Regulatory Networks
- Genetic Loci
- Histones/metabolism
- Humans
- Leukemia, Myeloid, Acute/genetics
- Mice, Inbred C57BL
- Mutation/genetics
- Nuclear Proteins/metabolism
- Nucleophosmin
- Principal Component Analysis
- Protein Processing, Post-Translational
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Transcription, Genetic
- fms-Like Tyrosine Kinase 3/metabolism
- Mice
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Affiliation(s)
- Haiyang Yun
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Nisha Narayan
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Shabana Vohra
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - George Giotopoulos
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Annalisa Mupo
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Pedro Madrigal
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Daniel Sasca
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Hematology, Oncology and Pneumology, University Medical Center Mainz, Mainz, Germany
| | - David Lara-Astiaso
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Sarah J Horton
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Shuchi Agrawal-Singh
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Eshwar Meduri
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Faisal Basheer
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Ludovica Marando
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Malgorzata Gozdecka
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Oliver M Dovey
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | | | - Xiaonan Wang
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Paolo Gallipoli
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Carsten Müller-Tidow
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Cameron S Osborne
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - George S Vassiliou
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Brian J P Huntly
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
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48
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Masselli E, Pozzi G, Carubbi C, Vitale M. The Genetic Makeup of Myeloproliferative Neoplasms: Role of Germline Variants in Defining Disease Risk, Phenotypic Diversity and Outcome. Cells 2021; 10:cells10102597. [PMID: 34685575 PMCID: PMC8534117 DOI: 10.3390/cells10102597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/06/2021] [Accepted: 09/24/2021] [Indexed: 12/14/2022] Open
Abstract
Myeloproliferative neoplasms are hematologic malignancies typified by a substantial heritable component. Germline variants may affect the risk of developing a MPN, as documented by GWAS studies on large patient cohorts. In addition, once the MPN occurred, inherited host genetic factors can be responsible for tuning the disease phenotypic presentation, outcome, and response to therapy. This review covered the polymorphisms that have been variably associated to MPNs, discussing them in the functional perspective of the biological pathways involved. Finally, we reviewed host genetic determinants of clonal hematopoiesis, a pre-malignant state that may anticipate overt hematologic neoplasms including MPNs.
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Affiliation(s)
- Elena Masselli
- Department of Medicine and Surgery, Anatomy Unit, University of Parma, 43126 Parma, Italy; (E.M.); (G.P.)
- University Hospital of Parma, AOU-PR, 43126 Parma, Italy
| | - Giulia Pozzi
- Department of Medicine and Surgery, Anatomy Unit, University of Parma, 43126 Parma, Italy; (E.M.); (G.P.)
| | - Cecilia Carubbi
- Department of Medicine and Surgery, Anatomy Unit, University of Parma, 43126 Parma, Italy; (E.M.); (G.P.)
- Correspondence: (C.C.); (M.V.)
| | - Marco Vitale
- Department of Medicine and Surgery, Anatomy Unit, University of Parma, 43126 Parma, Italy; (E.M.); (G.P.)
- University Hospital of Parma, AOU-PR, 43126 Parma, Italy
- Correspondence: (C.C.); (M.V.)
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49
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Ottema S, Mulet-Lazaro R, Erpelinck-Verschueren C, van Herk S, Havermans M, Arricibita Varea A, Vermeulen M, Beverloo HB, Gröschel S, Haferlach T, Haferlach C, J. Wouters B, Bindels E, Smeenk L, Delwel R. The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops. Nat Commun 2021; 12:5679. [PMID: 34584081 PMCID: PMC8479123 DOI: 10.1038/s41467-021-25862-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/02/2021] [Indexed: 02/08/2023] Open
Abstract
Chromosomal rearrangements are a frequent cause of oncogene deregulation in human malignancies. Overexpression of EVI1 is found in a subgroup of acute myeloid leukemia (AML) with 3q26 chromosomal rearrangements, which is often therapy resistant. In AMLs harboring a t(3;8)(q26;q24), we observed the translocation of a MYC super-enhancer (MYC SE) to the EVI1 locus. We generated an in vitro model mimicking a patient-based t(3;8)(q26;q24) using CRISPR-Cas9 technology and demonstrated hyperactivation of EVI1 by the hijacked MYC SE. This MYC SE contains multiple enhancer modules, of which only one recruits transcription factors active in early hematopoiesis. This enhancer module is critical for EVI1 overexpression as well as enhancer-promoter interaction. Multiple CTCF binding regions in the MYC SE facilitate this enhancer-promoter interaction, which also involves a CTCF binding site upstream of the EVI1 promoter. We hypothesize that this CTCF site acts as an enhancer-docking site in t(3;8) AML. Genomic analyses of other 3q26-rearranged AML patient cells point to a common mechanism by which EVI1 uses this docking site to hijack enhancers active in early hematopoiesis.
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Affiliation(s)
- Sophie Ottema
- grid.508717.c0000 0004 0637 3764Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands ,grid.499559.dOncode Institute, Utrecht, The Netherlands
| | - Roger Mulet-Lazaro
- grid.508717.c0000 0004 0637 3764Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands ,grid.499559.dOncode Institute, Utrecht, The Netherlands
| | - Claudia Erpelinck-Verschueren
- grid.508717.c0000 0004 0637 3764Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands ,grid.499559.dOncode Institute, Utrecht, The Netherlands
| | - Stanley van Herk
- grid.508717.c0000 0004 0637 3764Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands ,grid.499559.dOncode Institute, Utrecht, The Netherlands
| | - Marije Havermans
- grid.508717.c0000 0004 0637 3764Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands ,grid.499559.dOncode Institute, Utrecht, The Netherlands
| | - Andrea Arricibita Varea
- grid.508717.c0000 0004 0637 3764Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands ,grid.499559.dOncode Institute, Utrecht, The Netherlands
| | - Michael Vermeulen
- grid.508717.c0000 0004 0637 3764Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - H. Berna Beverloo
- grid.5645.2000000040459992XDepartment of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Stefan Gröschel
- grid.7497.d0000 0004 0492 0584A380, German Cancer Research Center, Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Torsten Haferlach
- grid.420057.40000 0004 7553 8497Munich Leukemia Laboratory, Munich, Germany
| | - Claudia Haferlach
- grid.420057.40000 0004 7553 8497Munich Leukemia Laboratory, Munich, Germany
| | - Bas J. Wouters
- grid.508717.c0000 0004 0637 3764Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands ,grid.499559.dOncode Institute, Utrecht, The Netherlands
| | - Eric Bindels
- grid.508717.c0000 0004 0637 3764Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Leonie Smeenk
- grid.508717.c0000 0004 0637 3764Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands ,grid.499559.dOncode Institute, Utrecht, The Netherlands
| | - Ruud Delwel
- grid.508717.c0000 0004 0637 3764Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands ,grid.499559.dOncode Institute, Utrecht, The Netherlands
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50
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Mizuno H, Koya J, Masamoto Y, Kagoya Y, Kurokawa M. Evi1 upregulates Fbp1 and supports progression of acute myeloid leukemia through pentose phosphate pathway activation. Cancer Sci 2021; 112:4112-4126. [PMID: 34363719 PMCID: PMC8486204 DOI: 10.1111/cas.15098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 07/17/2021] [Accepted: 08/03/2021] [Indexed: 01/14/2023] Open
Abstract
Evi1 is a transcription factor essential for the development as well as progression of acute myeloid leukemia (AML) and high Evi1 AML is associated with extremely poor clinical outcome. Since targeting metabolic vulnerability is the emerging therapeutic strategy of cancer, we herein investigated a novel therapeutic target of Evi1 by analyzing transcriptomic, epigenetic, and metabolomic profiling of mouse high Evi1 leukemia cells. We revealed that Evi1 overexpression and Evi1‐driven leukemic transformation upregulate transcription of gluconeogenesis enzyme Fbp1 and other pentose phosphate enzymes with interaction between Evi1 and the enhancer region of these genes. Metabolome analysis using Evi1‐overexpressing leukemia cells uncovered pentose phosphate pathway upregulation by Evi1 overexpression. Suppression of Fbp1 as well as pentose phosphate pathway enzymes by shRNA‐mediated knockdown selectively decreased Evi1‐driven leukemogenesis in vitro. Moreover, pharmacological or shRNA‐mediated Fbp1 inhibition in secondarily transplanted Evi1‐overexpressing leukemia mouse significantly decreased leukemia cell burden. Collectively, targeting FBP1 is a promising therapeutic strategy of high Evi1 AML.
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Affiliation(s)
- Hideaki Mizuno
- Department of Hematology and Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Junji Koya
- Department of Hematology and Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yosuke Masamoto
- Department of Hematology and Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yuki Kagoya
- Department of Hematology and Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mineo Kurokawa
- Department of Hematology and Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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