1
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Hussein R, Abou-Shanab AM, Badr E. A multi-omics approach for biomarker discovery in neuroblastoma: a network-based framework. NPJ Syst Biol Appl 2024; 10:52. [PMID: 38760476 PMCID: PMC11101461 DOI: 10.1038/s41540-024-00371-3] [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: 11/09/2023] [Accepted: 04/16/2024] [Indexed: 05/19/2024] Open
Abstract
Neuroblastoma (NB) is one of the leading causes of cancer-associated death in children. MYCN amplification is a prominent genetic marker for NB, and its targeting to halt NB progression is difficult to achieve. Therefore, an in-depth understanding of the molecular interactome of NB is needed to improve treatment outcomes. Analysis of NB multi-omics unravels valuable insight into the interplay between MYCN transcriptional and miRNA post-transcriptional modulation. Moreover, it aids in the identification of various miRNAs that participate in NB development and progression. This study proposes an integrated computational framework with three levels of high-throughput NB data (mRNA-seq, miRNA-seq, and methylation array). Similarity Network Fusion (SNF) and ranked SNF methods were utilized to identify essential genes and miRNAs. The specified genes included both miRNA-target genes and transcription factors (TFs). The interactions between TFs and miRNAs and between miRNAs and their target genes were retrieved where a regulatory network was developed. Finally, an interaction network-based analysis was performed to identify candidate biomarkers. The candidate biomarkers were further analyzed for their potential use in prognosis and diagnosis. The candidate biomarkers included three TFs and seven miRNAs. Four biomarkers have been previously studied and tested in NB, while the remaining identified biomarkers have known roles in other types of cancer. Although the specific molecular role is yet to be addressed, most identified biomarkers possess evidence of involvement in NB tumorigenesis. Analyzing cellular interactome to identify potential biomarkers is a promising approach that can contribute to optimizing efficient therapeutic regimens to target NB vulnerabilities.
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Affiliation(s)
- Rahma Hussein
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, 12578, Egypt
| | - Ahmed M Abou-Shanab
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, 12578, Egypt
| | - Eman Badr
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, 12578, Egypt.
- Faculty of Computers and Artificial Intelligence, Cairo University, Giza, 12613, Egypt.
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2
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Kao YR, Chen J, Kumari R, Ng A, Zintiridou A, Tatiparthy M, Ma Y, Aivalioti MM, Moulik D, Sundaravel S, Sun D, Reisz JA, Grimm J, Martinez-Lopez N, Stransky S, Sidoli S, Steidl U, Singh R, D'Alessandro A, Will B. An iron rheostat controls hematopoietic stem cell fate. Cell Stem Cell 2024; 31:378-397.e12. [PMID: 38402617 PMCID: PMC10939794 DOI: 10.1016/j.stem.2024.01.011] [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: 05/25/2023] [Revised: 12/20/2023] [Accepted: 01/30/2024] [Indexed: 02/27/2024]
Abstract
Mechanisms governing the maintenance of blood-producing hematopoietic stem and multipotent progenitor cells (HSPCs) are incompletely understood, particularly those regulating fate, ensuring long-term maintenance, and preventing aging-associated stem cell dysfunction. We uncovered a role for transitory free cytoplasmic iron as a rheostat for adult stem cell fate control. We found that HSPCs harbor comparatively small amounts of free iron and show the activation of a conserved molecular response to limited iron-particularly during mitosis. To study the functional and molecular consequences of iron restriction, we developed models allowing for transient iron bioavailability limitation and combined single-molecule RNA quantification, metabolomics, and single-cell transcriptomic analyses with functional studies. Our data reveal that the activation of the limited iron response triggers coordinated metabolic and epigenetic events, establishing stemness-conferring gene regulation. Notably, we find that aging-associated cytoplasmic iron loading reversibly attenuates iron-dependent cell fate control, explicating intervention strategies for dysfunctional aged stem cells.
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Affiliation(s)
- Yun-Ruei Kao
- Department of Oncology, Albert Einstein College of Medicine, New York, NY, USA.
| | - Jiahao Chen
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Rajni Kumari
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Anita Ng
- Karches Center for Oncology Research, the Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Aliona Zintiridou
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Madhuri Tatiparthy
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Yuhong Ma
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Maria M Aivalioti
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Deeposree Moulik
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Sriram Sundaravel
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Daqian Sun
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Julie A Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Juliane Grimm
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Nuria Martinez-Lopez
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Vatche and Tamar Manoukian Division of Digestive Diseases, University of California, Los Angeles, Los Angeles, CA, USA; Comprehensive Liver Research Center at University of California Los Angeles, CA, USA
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Ulrich Steidl
- Department of Oncology, Albert Einstein College of Medicine, New York, NY, USA; Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA; Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, New York, NY, USA; Blood Cancer Institute, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA; Cancer Dormancy and Tumor Microenvironment Institute, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rajat Singh
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Vatche and Tamar Manoukian Division of Digestive Diseases, University of California, Los Angeles, Los Angeles, CA, USA; Comprehensive Liver Research Center at University of California Los Angeles, CA, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Britta Will
- Department of Oncology, Albert Einstein College of Medicine, New York, NY, USA; Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA; Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, New York, NY, USA; Blood Cancer Institute, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA; Cancer Dormancy and Tumor Microenvironment Institute, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA; Institute for Aging Studies, Albert Einstein College of Medicine, New York, NY, USA.
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3
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Alvarez-Arzola R, Oliver L, Messmer MM, Twum DYF, Lee KP, Muhitch JB, Mesa C, Abrams SI. A Bacterial and Ganglioside-based Nanoparticle Initiates Reprogramming of Macrophages and Promotes Antitumor Phenotypes. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:475-486. [PMID: 38117752 DOI: 10.4049/jimmunol.2300256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 11/19/2023] [Indexed: 12/22/2023]
Abstract
Macrophages represent the most abundant immune component of the tumor microenvironment and often exhibit protumorigenic (M2-like) phenotypes that contribute to disease progression. Despite their generally accepted protumorigenic role, macrophages can also display tumoricidal (or M1-like) behavior, revealing that macrophages can be functionally reprogrammed, depending on the cues received within the tumor microenvironment. Moreover, such plasticity may be achieved by pharmacologic or biologic interventions. To that end, we previously demonstrated that a novel immunomodulator termed the "very small size particle" (VSSP) facilitates maturation of dendritic cells and differentiation of myeloid-derived suppressor cells to APCs with reduced suppressive activity in cancer models. VSSP was further shown to act in the bone marrow to drive the differentiation of progenitors toward monocytes, macrophages, and dendritic cells during emergency myelopoiesis. However, the underlying mechanisms for VSSP-driven alterations in myeloid differentiation and function remained unclear. In this study, in mouse models, we focused on macrophages and tested the hypothesis that VSSP drives macrophages toward M1-like functional states via IRF8- and PU.1-dependent mechanisms. We further hypothesized that such VSSP-mediated actions would be accompanied by enhanced antitumor responses. Overall, we showed that (1) VSSP drives naive or M2-derived macrophages to M1-like states, (2) the M1-like state induced by VSSP occurs via IRF8- and PU.1-dependent mechanisms, and (3) single-agent VSSP induces an antitumor response that is accompanied by alterations in the intratumoral myeloid compartment. These results provide a deeper mechanistic underpinning of VSSP and strengthen its use to drive M1-like responses in host defense, including cancer.
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Affiliation(s)
- Rydell Alvarez-Arzola
- Department of Immunoregulation, Immunology and Immunotherapy Direction, Center of Molecular Immunology, Havana, Cuba
| | - Liliana Oliver
- Department of Immunoregulation, Immunology and Immunotherapy Direction, Center of Molecular Immunology, Havana, Cuba
| | | | - Danielle Y F Twum
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Kelvin P Lee
- IU Simon Comprehensive Cancer Center, Division of Hematology/Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN
| | - Jason B Muhitch
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Circe Mesa
- Innovative Immunotherapy Alliance S.A., Mariel, Artemisa, Cuba
| | - Scott I Abrams
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY
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4
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Klein DC, Lardo SM, Hainer SJ. The ncBAF Complex Regulates Transcription in AML Through H3K27ac Sensing by BRD9. CANCER RESEARCH COMMUNICATIONS 2024; 4:237-252. [PMID: 38126767 PMCID: PMC10831031 DOI: 10.1158/2767-9764.crc-23-0382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/02/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023]
Abstract
The non-canonical BAF complex (ncBAF) subunit BRD9 is essential for acute myeloid leukemia (AML) cell viability but has an unclear role in leukemogenesis. Because BRD9 is required for ncBAF complex assembly through its DUF3512 domain, precise bromodomain inhibition is necessary to parse the role of BRD9 as a transcriptional regulator from that of a scaffolding protein. To understand the role of BRD9 bromodomain function in regulating AML, we selected a panel of five AML cell lines with distinct driver mutations, disease classifications, and genomic aberrations and subjected these cells to short-term BRD9 bromodomain inhibition. We examined the bromodomain-dependent growth of these cell lines, identifying a dependency in AML cell lines but not HEK293T cells. To define a mechanism through which BRD9 maintains AML cell survival, we examined nascent transcription, chromatin accessibility, and ncBAF complex binding genome-wide after bromodomain inhibition. We identified extensive regulation of transcription by BRD9 bromodomain activity, including repression of myeloid maturation factors and tumor suppressor genes, while standard AML chemotherapy targets were repressed by inhibition of the BRD9 bromodomain. BRD9 bromodomain activity maintained accessible chromatin at both gene promoters and gene-distal putative enhancer regions, in a manner that qualitatively correlated with enrichment of BRD9 binding. Furthermore, we identified reduced chromatin accessibility at GATA, ETS, and AP-1 motifs and increased chromatin accessibility at SNAIL-, HIC-, and TP53-recognized motifs after BRD9 inhibition. These data suggest a role for BRD9 in regulating AML cell differentiation through modulation of accessibility at hematopoietic transcription factor binding sites. SIGNIFICANCE The bromodomain-containing protein BRD9 is essential for AML cell viability, but it is unclear whether this requirement is due to the protein's role as an epigenetic reader. We inhibited this activity and identified altered gene-distal chromatin regulation and transcription consistent with a more mature myeloid cell state.
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Affiliation(s)
- David C. Klein
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Santana M. Lardo
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Sarah J. Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
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5
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Martinez TC, McNerney ME. Haploinsufficient Transcription Factors in Myeloid Neoplasms. ANNUAL REVIEW OF PATHOLOGY 2024; 19:571-598. [PMID: 37906947 DOI: 10.1146/annurev-pathmechdis-051222-013421] [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] [Indexed: 11/02/2023]
Abstract
Many transcription factors (TFs) function as tumor suppressor genes with heterozygous phenotypes, yet haploinsufficiency generally has an underappreciated role in neoplasia. This is no less true in myeloid cells, which are normally regulated by a delicately balanced and interconnected transcriptional network. Detailed understanding of TF dose in this circuitry sheds light on the leukemic transcriptome. In this review, we discuss the emerging features of haploinsufficient transcription factors (HITFs). We posit that: (a) monoallelic and biallelic losses can have distinct cellular outcomes; (b) the activity of a TF exists in a greater range than the traditional Mendelian genetic doses; and (c) how a TF is deleted or mutated impacts the cellular phenotype. The net effect of a HITF is a myeloid differentiation block and increased intercellular heterogeneity in the course of myeloid neoplasia.
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Affiliation(s)
- Tanner C Martinez
- Department of Pathology, Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago Medicine Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois, USA;
- Medical Scientist Training Program, The University of Chicago, Chicago, Illinois, USA
| | - Megan E McNerney
- Department of Pathology, Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago Medicine Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois, USA;
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6
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Qiu K, Vu D, Wang L, Bookstaver A, Dinh TN, Goldfarb AN, Tenen DG, Trinh BQ. Chromatin structure and 3D architecture define differential functions of PU.1 cis regulatory elements in human blood cell lineages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.01.573782. [PMID: 38260486 PMCID: PMC10802337 DOI: 10.1101/2024.01.01.573782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The precise spatio-temporal expression of the hematopoietic ETS transcription factor PU.1 that determines the hematopoietic cell fates is tightly regulated at the chromatin level. However, it remains elusive as to how chromatin signatures are linked to this dynamic expression pattern of PU.1 across blood cell lineages. Here we performed an unbiased and in-depth analysis of the relationship between human PU.1 expression, the presence of trans-acting factors, and 3D architecture at various cis-regulatory elements (CRE) proximal to the PU.1 locus. We identified multiple novel CREs at the upstream region of the gene following an integrative inspection for conserved DNA elements at the chromatin-accessible regions in primary human blood lineages. We showed that a subset of CREs localize within a 10 kb-wide cluster that exhibits that exhibit molecular features of a myeloid-specific super-enhancer involved in mediating PU.1 autoregulation, including open chromatin, unmethylated DNA, histone enhancer marks, transcription of enhancer RNAs, and occupancy of the PU.1 protein itself. Importantly, we revealed the presence of common 35-kb-wide CTCF-bound insulated neighborhood that contains the CRE cluster, forming the chromatin territory for lineage-specific and CRE-mediated chromatin interactions. These include functional CRE-promoter interactions in myeloid and B cells but not in erythroid and T cells. Our findings also provide mechanistic insights into the interplay between dynamic chromatin structure and 3D architecture in defining certain CREs as enhancers or silencers in chromatin regulation of PU.1 expression. The study lays the groundwork for further examination of PU.1 CREs as well as epigenetic regulation in malignant hematopoiesis.
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7
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Pawlikowska P, Delestré L, Gregoricchio S, Oppezzo A, Esposito M, Diop MB, Rosselli F, Guillouf C. FANCA deficiency promotes leukaemic progression by allowing the emergence of cells carrying oncogenic driver mutations. Oncogene 2023; 42:2764-2775. [PMID: 37573408 PMCID: PMC10491493 DOI: 10.1038/s41388-023-02800-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 07/21/2023] [Accepted: 07/28/2023] [Indexed: 08/14/2023]
Abstract
Leukaemia is caused by the clonal evolution of a cell that accumulates mutations/genomic rearrangements, allowing unrestrained cell growth. However, recent identification of leukaemic mutations in the blood cells of healthy individuals revealed that additional events are required to expand the mutated clones for overt leukaemia. Here, we assessed the functional consequences of deleting the Fanconi anaemia A (Fanca) gene, which encodes a DNA damage response protein, in Spi1 transgenic mice that develop preleukaemic syndrome. FANCA loss increases SPI1-associated disease penetrance and leukaemic progression without increasing the global mutation load of leukaemic clones. However, a high frequency of leukaemic FANCA-depleted cells display heterozygous activating mutations in known oncogenes, such as Kit or Nras, also identified but at low frequency in FANCA-WT mice with preleukaemic syndrome, indicating that FANCA counteracts the emergence of oncogene mutated leukaemic cells. A unique transcriptional signature is associated with the leukaemic status of FANCA-depleted cells, leading to activation of MDM4, NOTCH and Wnt/β-catenin pathways. We show that NOTCH signalling improves the proliferation capacity of FANCA-deficient leukaemic cells. Collectively, our observations indicate that loss of the FANC pathway, known to control genetic instability, fosters the expansion of leukaemic cells carrying oncogenic mutations rather than mutation formation. FANCA loss may contribute to this leukaemogenic progression by reprogramming transcriptomic landscape of the cells.
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Affiliation(s)
- Patrycja Pawlikowska
- CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Villejuif, France
- Inserm U981, Gustave Roussy Cancer Campus, CNRS UMS3655, Inserm US23AMMICA, Villejuif, France
| | - Laure Delestré
- Equipe Labellisée Ligue Nationale Contre le Cancer, Villejuif, France
- Inserm UMR1170, Université Paris-Saclay, Gustave Roussy Cancer Campus, Villejuif, France
| | - Sebastian Gregoricchio
- Equipe Labellisée Ligue Nationale Contre le Cancer, Villejuif, France
- Inserm UMR1170, Université Paris-Saclay, Gustave Roussy Cancer Campus, Villejuif, France
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Alessia Oppezzo
- CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Villejuif, France
| | - Michela Esposito
- Equipe Labellisée Ligue Nationale Contre le Cancer, Villejuif, France
- Inserm UMR1170, Université Paris-Saclay, Gustave Roussy Cancer Campus, Villejuif, France
| | - M' Boyba Diop
- Equipe Labellisée Ligue Nationale Contre le Cancer, Villejuif, France
- Inserm UMR1170, Université Paris-Saclay, Gustave Roussy Cancer Campus, Villejuif, France
| | - Filippo Rosselli
- CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, Villejuif, France.
- Equipe Labellisée Ligue Nationale Contre le Cancer, Villejuif, France.
| | - Christel Guillouf
- Equipe Labellisée Ligue Nationale Contre le Cancer, Villejuif, France.
- Inserm UMR1170, Université Paris-Saclay, Gustave Roussy Cancer Campus, Villejuif, France.
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8
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Wei Z, Su L, Gao S. The roles of ubiquitination in AML. Ann Hematol 2023:10.1007/s00277-023-05415-y. [PMID: 37603061 DOI: 10.1007/s00277-023-05415-y] [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: 04/25/2023] [Accepted: 08/10/2023] [Indexed: 08/22/2023]
Abstract
Acute myeloid leukemia (AML) is a heterogeneously malignant disorder resulting in poor prognosis. Ubiquitination, a major post-translational modification (PTM), plays an essential role in regulating various cellular processes and determining cell fate. Despite these initial insights, the precise role of ubiquitination in AML pathogenesis and treatment remains largely unknown. In order to address this knowledge gap, we explore the relationship between ubiquitination and AML from the perspectives of signal transduction, cell differentiation, and cell cycle control; and try to find out how this relationship can be utilized to inform new therapeutic strategies for AML patients.
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Affiliation(s)
- Zhifeng Wei
- Department of Hematology, The First Hospital of Jilin University, Changchun, China
| | - Long Su
- Department of Hematology, The First Hospital of Jilin University, Changchun, China
| | - Sujun Gao
- Department of Hematology, The First Hospital of Jilin University, Changchun, China.
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9
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Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK. DNA selection by the master transcription factor PU.1. Cell Rep 2023; 42:112671. [PMID: 37352101 PMCID: PMC10479921 DOI: 10.1016/j.celrep.2023.112671] [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: 12/13/2022] [Revised: 04/07/2023] [Accepted: 06/02/2023] [Indexed: 06/25/2023] Open
Abstract
The master transcriptional regulator PU.1/Spi-1 engages DNA sites with affinities spanning multiple orders of magnitude. To elucidate this remarkable plasticity, we have characterized 22 high-resolution co-crystallographic PU.1/DNA complexes across the addressable affinity range in myeloid gene transactivation. Over a purine-rich core (such as 5'-GGAA-3') flanked by variable sequences, affinity is negotiated by direct readout on the 5' flank via a critical glutamine (Q226) sidechain and by indirect readout on the 3' flank by sequence-dependent helical flexibility. Direct readout by Q226 dynamically specifies PU.1's characteristic preference for purines and explains the pathogenic mutation Q226E in Waldenström macroglobulinemia. The structures also reveal how disruption of Q226 mediates strand-specific inhibition by DNA methylation and the recognition of non-canonical sites, including the authentic binding sequence at the CD11b promoter. A re-synthesis of phylogenetic and structural data on the ETS family, considering the centrality of Q226 in PU.1, unifies the model of DNA selection by ETS proteins.
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Affiliation(s)
- J Ross Terrell
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Samuel J Taylor
- Departments of Cell Biology, Oncology, and Medicine, Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Blood Cancer Institute, and the Montefiore Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Amelia L Schneider
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Yue Lu
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Tyler N Vernon
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Suela Xhani
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Ryan H Gumpper
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Ming Luo
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Ulrich Steidl
- Departments of Cell Biology, Oncology, and Medicine, Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Blood Cancer Institute, and the Montefiore Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
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10
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Chavez JS, Rabe JL, Niño KE, Wells HH, Gessner RL, Mills TS, Hernandez G, Pietras EM. PU.1 is required to restrain myelopoiesis during chronic inflammatory stress. Front Cell Dev Biol 2023; 11:1204160. [PMID: 37497478 PMCID: PMC10368259 DOI: 10.3389/fcell.2023.1204160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/19/2023] [Indexed: 07/28/2023] Open
Abstract
Chronic inflammation is a common feature of aging and numerous diseases such as diabetes, obesity, and autoimmune syndromes and has been linked to the development of hematological malignancy. Blood-forming hematopoietic stem cells (HSC) can contribute to these diseases via the production of tissue-damaging myeloid cells and/or the acquisition of mutations in epigenetic and transcriptional regulators that initiate evolution toward leukemogenesis. We previously showed that the myeloid "master regulator" transcription factor PU.1 is robustly induced in HSC by pro-inflammatory cytokines such as interleukin (IL)-1β and limits their proliferative activity. Here, we used a PU.1-deficient mouse model to investigate the broader role of PU.1 in regulating hematopoietic activity in response to chronic inflammatory challenges. We found that PU.1 is critical in restraining inflammatory myelopoiesis via suppression of cell cycle and self-renewal gene programs in myeloid-biased multipotent progenitor (MPP) cells. Our data show that while PU.1 functions as a key driver of myeloid differentiation, it plays an equally critical role in tailoring hematopoietic responses to inflammatory stimuli while limiting expansion and self-renewal gene expression in MPPs. These data identify PU.1 as a key regulator of "emergency" myelopoiesis relevant to inflammatory disease and leukemogenesis.
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Affiliation(s)
- James S. Chavez
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Jennifer L. Rabe
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Katia E. Niño
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Harrison H. Wells
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Rachel L. Gessner
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Taylor S. Mills
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Giovanny Hernandez
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Eric M. Pietras
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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11
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Srinivasan Rajsri K, Roy N, Chakraborty S. Acute Myeloid Leukemia Stem Cells in Minimal/Measurable Residual Disease Detection. Cancers (Basel) 2023; 15:2866. [PMID: 37345204 PMCID: PMC10216329 DOI: 10.3390/cancers15102866] [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: 04/06/2023] [Revised: 05/14/2023] [Accepted: 05/17/2023] [Indexed: 06/23/2023] Open
Abstract
Acute myeloid leukemia (AML) is a hematological malignancy characterized by an abundance of incompletely matured or immature clonally derived hematopoietic precursors called leukemic blasts. Rare leukemia stem cells (LSCs) that can self-renew as well as give rise to leukemic progenitors comprising the bulk of leukemic blasts are considered the cellular reservoir of disease initiation and maintenance. LSCs are widely thought to be relatively resistant as well as adaptive to chemotherapy and can cause disease relapse. Therefore, it is imperative to understand the molecular bases of LSC forms and functions during different stages of disease progression, so we can more accurately identify these cells and design therapies to target them. Irrespective of the morphological, cytogenetic, and cellular heterogeneity of AML, the uniform, singularly important and independently significant prognosticator of disease response to therapy and patient outcome is measurable or minimal residual disease (MRD) detection, defined by residual disease detection below the morphology-based 5% blast threshold. The importance of LSC identification and frequency estimation during MRD detection, in order to make MRD more effective in predicting disease relapse and modifying therapeutic regimen is becoming increasingly apparent. This review focuses on summarizing functional and cellular composition-based LSC identification and linking those studies to current techniques of MRD detection to suggest LSC-inclusive MRD detection as well as outline outstanding questions that need to be addressed to improve the future of AML clinical management and treatment outcomes.
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Affiliation(s)
- Kritika Srinivasan Rajsri
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; (K.S.R.); (N.R.)
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY 10010, USA
| | - Nainita Roy
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; (K.S.R.); (N.R.)
| | - Sohini Chakraborty
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; (K.S.R.); (N.R.)
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12
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Ueda K. Review: MDMX plays a central role in leukemic transformation and may be a promising target for leukemia prevention strategies. Exp Hematol 2023:S0301-472X(23)00161-3. [PMID: 37086813 DOI: 10.1016/j.exphem.2023.04.001] [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: 03/19/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 04/24/2023]
Abstract
Acute myeloid leukemia (AML) is a fatal disease resulting from preleukemic hematopoietic conditions including asymptomatic clonal hematopoiesis. The accumulation of genetic changes is one of the causes of leukemic transformation. However, nongenetic factors including the overexpression of specific genes also contribute to preleukemic to leukemic transition. Among them, the p53 inhibitor Murine Double Minute X (MDMX) plays crucial roles especially in leukemia initiation. MDMX is broadly overexpressed in vast majority of AML cases, including in hematopoietic stem/progenitor cell (HSPC) level. Recently, high expression of MDMX in HSPC has been shown to be associated with leukemic transformation in patients with myelodysplastic syndromes, and preclinical studies demonstrated that MDMX overexpression accelerates the transformation of preleukemic murine models, including models of clonal hematopoiesis. MDMX inhibition, through activation of cell-intrinsic p53 activity, shows antileukemic effects. However, the molecular mechanisms of MDMX in provoking leukemic transformation are complicated. Both p53-dependent and independent mechanisms are involved in the progression of the disease. This review discusses the canonical and noncanonical functions of MDMX and how these functions are involved in the maintenance, expansion, and progression to malignancy of preleukemic stem cells. Moreover, strategies on how leukemic transformation could possibly be prevented by targeting MDMX in preleukemic stem cells are discussed.
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Affiliation(s)
- Koki Ueda
- Department of Blood Transfusion and Transplantation Immunology, Fukushima Medical University, Fukushima, Fukushima 9601295, Japan; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
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13
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Saultz JN, Tyner JW. Chasing leukemia differentiation through induction therapy, relapse and transplantation. Blood Rev 2023; 57:101000. [PMID: 36041918 DOI: 10.1016/j.blre.2022.101000] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/23/2022] [Accepted: 08/09/2022] [Indexed: 01/28/2023]
Abstract
Despite rapid advances in our understanding of acute myeloid leukemia (AML), the disease remains challenging to treat with 5-year survival for adult patients 20 years or older estimated to be 26% (Cancer 2021). The use of new targeted therapies including BCL2, IDH1/IDH2, and FLT3 inhibitors has revolutionized treatment approaches but also changed the disease trajectory with unique modes of resistance. Recent studies have shown that stem cell maturation state drives expression level and/or dependence on various pathways, critical to determining drug response. Instead of anticipating these changes, we remain behind the curve chasing the next expanded clone. This review will focus on current approaches to treatment in AML, including defining the significance of blast differentiation state on chemotherapeutic response, signaling pathway dependence, metabolism, immune response, and phenotypic changes. We conclude that multimodal treatment approaches are necessary to target both the immature and mature clones, thereby, sustaining drug response.
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Affiliation(s)
- Jennifer N Saultz
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, United States of America; Division of Hematology and Medical Oncology, Oregon Health and Science University, Portland, OR, United States of America.
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, United States of America; Division of Hematology and Medical Oncology, Oregon Health and Science University, Portland, OR, United States of America; Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, OR, United States of America
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14
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von Knebel Doeberitz N, Paech D, Sturm D, Pusch S, Turcan S, Saunthararajah Y. Changing paradigms in oncology: Toward noncytotoxic treatments for advanced gliomas. Int J Cancer 2022; 151:1431-1446. [PMID: 35603902 PMCID: PMC9474618 DOI: 10.1002/ijc.34131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/25/2022]
Abstract
Glial-lineage malignancies (gliomas) recurrently mutate and/or delete the master regulators of apoptosis p53 and/or p16/CDKN2A, undermining apoptosis-intending (cytotoxic) treatments. By contrast to disrupted p53/p16, glioma cells are live-wired with the master transcription factor circuits that specify and drive glial lineage fates: these transcription factors activate early-glial and replication programs as expected, but fail in their other usual function of forcing onward glial lineage-maturation-late-glial genes have constitutively "closed" chromatin requiring chromatin-remodeling for activation-glioma-genesis disrupts several epigenetic components needed to perform this work, and simultaneously amplifies repressing epigenetic machinery instead. Pharmacologic inhibition of repressing epigenetic enzymes thus allows activation of late-glial genes and terminates glioma self-replication (self-replication = replication without lineage-maturation), independent of p53/p16/apoptosis. Lineage-specifying master transcription factors therefore contrast with p53/p16 in being enriched in self-replicating glioma cells, reveal a cause-effect relationship between aberrant epigenetic repression of late-lineage programs and malignant self-replication, and point to specific epigenetic targets for noncytotoxic glioma-therapy.
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Affiliation(s)
| | - Daniel Paech
- Division of RadiologyGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Department of NeuroradiologyBonn University HospitalBonnGermany
| | - Dominik Sturm
- Hopp Children's Cancer Center (KiTZ) HeidelbergHeidelbergGermany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK)HeidelbergGermany
- Department of Pediatric Oncology, Hematology & ImmunologyHeidelberg University HospitalHeidelbergGermany
| | - Stefan Pusch
- Department of NeuropathologyInstitute of Pathology, Ruprecht‐Karls‐University HeidelbergHeidelbergGermany
- German Cancer Consortium (DKTK), Clinical Cooperation Unit (CCU) Neuropathology, German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Sevin Turcan
- Department of NeurologyHeidelberg University HospitalHeidelbergGermany
| | - Yogen Saunthararajah
- Department of Translational Hematology and Oncology ResearchTaussig Cancer Institute, Cleveland ClinicClevelandOhioUSA
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15
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Pingul BY, Huang H, Chen Q, Alikarami F, Zhang Z, Qi J, Bernt KM, Berger SL, Cao Z, Shi J. Dissection of the MEF2D-IRF8 transcriptional circuit dependency in acute myeloid leukemia. iScience 2022; 25:105139. [PMID: 36193052 PMCID: PMC9526175 DOI: 10.1016/j.isci.2022.105139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 08/05/2022] [Accepted: 09/10/2022] [Indexed: 11/26/2022] Open
Abstract
Transcriptional dysregulation is a prominent feature in leukemia. Here, we systematically surveyed transcription factor (TF) vulnerabilities in leukemia and uncovered TF clusters that exhibit context-specific vulnerabilities within and between different subtypes of leukemia. Among these TF clusters, we demonstrated that acute myeloid leukemia (AML) with high IRF8 expression was addicted to MEF2D. MEF2D and IRF8 form an autoregulatory loop via direct binding to mutual enhancer elements. One important function of this circuit in AML is to sustain PU.1/MEIS1 co-regulated transcriptional outputs via stabilizing PU.1’s chromatin occupancy. We illustrated that AML could acquire dependency on this circuit through various oncogenic mechanisms that results in the activation of their enhancers. In addition to forming a circuit, MEF2D and IRF8 can also separately regulate gene expression, and dual perturbation of these two TFs leads to a more robust inhibition of AML proliferation. Collectively, our results revealed a TF circuit essential for AML survival. MEF2D is a context-specific vulnerability in IRF8hi AML MEF2D and IRF8 form a transcriptional circuit via binding to each other’s enhancers MEF2D-IRF8 circuit supports PU.1’s chromatin occupancy and transcriptional output MEF2D and IRF8 can regulate separate gene expression programs alongside the circuit
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16
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Schleicher WE, Pietras EM. Reduced PU.1 Expression Collaborates with Tet2 Loss to Trigger Myeloid Leukemogenesis. Blood Cancer Discov 2022; 3:378-381. [PMID: 36065607 PMCID: PMC9445751 DOI: 10.1158/2643-3230.bcd-22-0100] [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] [Indexed: 11/16/2022] Open
Abstract
The leukemic transformation of hematopoietic stem and progenitor cells in the setting of Tet2 deficiency is driven by PU.1 gene network loss through complementary reduction in PU.1 expression and hypermethylation of ETS loci at the enhancers of PU.1 target genes. See related article by Aivalioti et al., p. 444 (6).
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Affiliation(s)
- Wolfgang E. Schleicher
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Eric M. Pietras
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
- Department of Microbiology and Immunology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
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17
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Aivalioti MM, Bartholdy BA, Pradhan K, Bhagat TD, Zintiridou A, Jeong JJ, Thiruthuvanathan VJ, Pujato M, Paranjpe A, Zhang C, Levine RL, Viny AD, Wickrema A, Verma A, Will B. PU.1-Dependent Enhancer Inhibition Separates Tet2-Deficient Hematopoiesis from Malignant Transformation. Blood Cancer Discov 2022; 3:444-467. [PMID: 35820129 PMCID: PMC9894728 DOI: 10.1158/2643-3230.bcd-21-0226] [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: 12/12/2021] [Revised: 04/05/2022] [Accepted: 07/07/2022] [Indexed: 12/17/2022] Open
Abstract
Cytosine hypermethylation in and around DNA-binding sites of master transcription factors, including PU.1, occurs in aging hematopoietic stem cells following acquired loss-of-function mutations of DNA methyl-cytosine dioxygenase ten-eleven translocation-2 (TET2), albeit functional relevance has been unclear. We show that Tet2-deficient mouse hematopoietic stem and progenitor cells undergo malignant transformation upon compromised gene regulation through heterozygous deletion of an upstream regulatory region (UREΔ/WT) of the PU.1 gene. Although compatible with multilineage blood formation at young age, Tet2-deficient PU.1 UREΔ/WT mice develop highly penetrant, transplantable acute myeloid leukemia (AML) during aging. Leukemic stem and progenitor cells show hypermethylation at putative PU.1-binding sites, fail to activate myeloid enhancers, and are hallmarked by a signature of genes with impaired expression shared with human AML. Our study demonstrates that Tet2 and PU.1 jointly suppress leukemogenesis and uncovers a methylation-sensitive PU.1-dependent gene network as a unifying molecular vulnerability associated with AML. SIGNIFICANCE We identify moderately impaired PU.1 mRNA expression as a biological modality predisposing Tet2-deficient hematopoietic stem and progenitor cells to malignant transformation. Our study furthermore uncovers a methylation-sensitive PU.1 gene network as a common feature of myeloid leukemia potentially allowing for the identification of patients at risk for malignant transformation. See related commentary by Schleicher and Pietras, p. 378. This article is highlighted in the In This Issue feature, p. 369.
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Affiliation(s)
- Maria M Aivalioti
- Department of Cell Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
- Graduate Programs in the Biomedical Sciences, Albert Einstein College of Medicine, Bronx, New York
| | - Boris A Bartholdy
- Department of Cell Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| | - Kith Pradhan
- Department of Medicine (Oncology), Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| | - Tushar D Bhagat
- Department of Medicine (Oncology), Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| | - Aliona Zintiridou
- Department of Cell Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| | - Jong Jin Jeong
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Victor J Thiruthuvanathan
- Department of Cell Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| | - Mario Pujato
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Aditi Paranjpe
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Chi Zhang
- Department of Cell Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| | - Ross L Levine
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Aaron D Viny
- Department of Genetics and Development, Columbia University, New York, New York
| | - Amittha Wickrema
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Amit Verma
- Department of Medicine (Oncology), Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| | - Britta Will
- Department of Cell Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
- Department of Medicine (Oncology), Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
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18
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Bašová P, Paszeková H, Minařík L, Dluhošová M, Burda P, Stopka T. Combined Approach to Leukemic Differentiation Using Transcription Factor PU.1-Enhancing Agents. Int J Mol Sci 2022; 23:ijms23126729. [PMID: 35743167 PMCID: PMC9224232 DOI: 10.3390/ijms23126729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 02/04/2023] Open
Abstract
The transcription factor PU.1 (Purine-rich DNA binding, SPI1) is a key regulator of hematopoiesis, whose level is influenced by transcription through its enhancers and its post-transcriptional degradation via microRNA-155 (miR-155). The degree of transcriptional regulation of the PU.1 gene is influenced by repression via DNA methylation, as well as other epigenetic factors, such as those related to progenitor maturation status, which is modulated by the transcription factor Myeloblastosis oncogene (MYB). In this work, we show that combinatorial treatment of acute myeloid leukemia (AML) cells with DNA methylation inhibitors (5-Azacytidine), MYB inhibitors (Celastrol), and anti-miR-155 (AM155) ideally leads to overproduction of PU.1. We also show that PU.1 reactivation can be compensated by miR-155 and that only a combined approach leads to sustained PU.1 derepression, even at the protein level. The triple effect on increasing PU.1 levels in myeloblasts stimulates the myeloid transcriptional program while inhibiting cell survival and proliferation, leading to partial leukemic differentiation.
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19
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Gupta M, Will B. SEPHguarding acute myeloid leukemia. Cell Stem Cell 2022; 29:350-352. [PMID: 35245465 DOI: 10.1016/j.stem.2022.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Adaptive aberrant gene regulation is a hallmark of malignant growth and therapy resistance in acute myeloid leukemia (AML). In this issue of Cell Stem Cell, Eagle et al. identified oncogenic enhancer-driven overexpression of selenophosphate synthetase 2 (SEPHS2) as an opportunity for targeted mitigation of malignant cell growth in AML.
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Affiliation(s)
- Malini Gupta
- Department of Cell Biology, Albert Einstein College of Medicine, NY, USA
| | - Britta Will
- Department of Cell Biology, Albert Einstein College of Medicine, NY, USA; Montefiore-Einstein Cancer Center, Albert Einstein College of Medicine / Montefiore Medical Center, NY, USA.
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20
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Chavez JS, Rabe JL, Hernandez G, Mills TS, Niño KE, Davizon-Castillo P, Pietras EM. PU.1 Expression Defines Distinct Functional Activities in the Phenotypic HSC Compartment of a Murine Inflammatory Stress Model. Cells 2022; 11:cells11040680. [PMID: 35203330 PMCID: PMC8870714 DOI: 10.3390/cells11040680] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/05/2022] [Accepted: 02/10/2022] [Indexed: 12/17/2022] Open
Abstract
The transcription factor PU.1 is a critical regulator of lineage fate in blood-forming hematopoietic stem cells (HSC). In response to pro-inflammatory signals, such as the cytokine IL-1β, PU.1 expression is increased in HSC and is associated with myeloid lineage expansion. To address potential functional heterogeneities arising in the phenotypic HSC compartment due to changes in PU.1 expression, here, we fractionated phenotypic HSC in mice using the SLAM surface marker code in conjunction with PU.1 expression levels, using the PU.1-EYFP reporter mouse strain. While PU.1lo SLAM cells contain extensive long-term repopulating activity and a molecular signature corresponding to HSC activity at steady state, following IL-1β treatment, HSCLT induce PU.1 expression and are replaced in the PU.1lo SLAM fraction by CD41+ HSC-like megakaryocytic progenitors (SL-MkP) with limited long-term engraftment capacity. On the other hand, the PU.1hi SLAM fraction exhibits extensive myeloid lineage priming and clonogenic activity and expands rapidly in response to IL-1β. Furthermore, we show that EPCR expression, but not CD150 expression, can distinguish HSCLT and SL-MkP under inflammatory conditions. Altogether, our data provide insights into the dynamic regulation of PU.1 and identify how PU.1 levels are linked to HSC fate in steady state and inflammatory stress conditions.
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Affiliation(s)
- James S. Chavez
- Division of Hematology, Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, USA; (J.S.C.); (J.L.R.); (G.H.); (T.S.M.); (K.E.N.)
| | - Jennifer L. Rabe
- Division of Hematology, Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, USA; (J.S.C.); (J.L.R.); (G.H.); (T.S.M.); (K.E.N.)
| | - Giovanny Hernandez
- Division of Hematology, Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, USA; (J.S.C.); (J.L.R.); (G.H.); (T.S.M.); (K.E.N.)
| | - Taylor S. Mills
- Division of Hematology, Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, USA; (J.S.C.); (J.L.R.); (G.H.); (T.S.M.); (K.E.N.)
| | - Katia E. Niño
- Division of Hematology, Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, USA; (J.S.C.); (J.L.R.); (G.H.); (T.S.M.); (K.E.N.)
| | - Pavel Davizon-Castillo
- Department of Pediatrics, Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, USA;
| | - Eric M. Pietras
- Division of Hematology, Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, USA; (J.S.C.); (J.L.R.); (G.H.); (T.S.M.); (K.E.N.)
- Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, USA
- Correspondence:
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21
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Almohsen F, Al-Rubaie HA, Habib MA, Nasr SA, Perni R, Al-Quraishi L. Circulating miR-126-3p and miR-423-5p Expression in de novo Adult Acute Myeloid Leukemia: Correlations with Response to Induction Therapy and the 2-Year Overall Survival. J Blood Med 2022; 13:83-92. [PMID: 35210895 PMCID: PMC8863343 DOI: 10.2147/jbm.s347397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/20/2022] [Indexed: 12/02/2022] Open
Abstract
Background Purpose Patients and Methods Results Conclusion
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Affiliation(s)
- Faez Almohsen
- College of Medicine, University of Baghdad, Baghdad, Iraq
- Correspondence: Faez Almohsen, College of Medicine, University of Baghdad, Baghdad, Iraq, Tel +964 7902834062, Email
| | | | - Manal A Habib
- College of Medicine, University of Baghdad, Baghdad, Iraq
| | - Sherif A Nasr
- siParadigm Diagnostic Informatics, New Jersey, NJ, USA
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22
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Da Ros F, Persano L, Bizzotto D, Michieli M, Braghetta P, Mazzucato M, Bonaldo P. Emilin-2 is a component of bone marrow extracellular matrix regulating mesenchymal stem cell differentiation and hematopoietic progenitors. Stem Cell Res Ther 2022; 13:2. [PMID: 35012633 PMCID: PMC8744352 DOI: 10.1186/s13287-021-02674-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/09/2021] [Indexed: 02/08/2023] Open
Abstract
Background Dissection of mechanisms involved in the regulation of bone marrow microenvironment through cell–cell and cell–matrix contacts is essential for the detailed understanding of processes underlying bone marrow activities both under physiological conditions and in hematologic malignancies. Here we describe Emilin-2 as an abundant extracellular matrix component of bone marrow stroma. Methods Immunodetection of Emilin-2 was performed in bone marrow sections of mice from 30 days to 6 months of age. Emilin-2 expression was monitored in vitro in primary and mesenchymal stem cell lines under undifferentiated and adipogenic conditions. Hematopoietic stem cells and progenitors in bone marrow of 3- to 10-month-old wild-type and Emilin-2 null mice were analyzed by flow cytometry. Results Emilin-2 is deposited in bone marrow extracellular matrix in an age-dependent manner, forming a meshwork that extends from compact bone boundaries to the central trabecular regions. Emilin-2 is expressed and secreted by both primary and immortalized bone marrow mesenchymal stem cells, exerting an inhibitory action in adipogenic differentiation. In vivo Emilin-2 deficiency impairs the frequency of hematopoietic stem/progenitor cells in bone marrow during aging. Conclusion Our data provide new insights in the contribution of bone marrow extracellular matrix microenvironment in the regulation of stem cell niches and hematopoietic progenitor differentiation. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-021-02674-2.
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Affiliation(s)
- Francesco Da Ros
- SOSd Cell Stem Unit, Department of Translational Research, National Cancer Center CRO-IRCSS, 33081, Aviano, Italy.,Department of Molecular Medicine, University of Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy
| | - Luca Persano
- Department of Women's and Children's Health, University of Padova, 35131, Padova, Italy.,IRP - Pediatric Research Institute, 35131, Padova, Italy
| | - Dario Bizzotto
- Department of Molecular Medicine, University of Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy
| | - Mariagrazia Michieli
- SOSd Cell Therapy and High Dose Chemotherapy, National Cancer Center CRO- IRCCS, 33081, Aviano, Italy
| | - Paola Braghetta
- Department of Molecular Medicine, University of Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy
| | - Mario Mazzucato
- SOSd Cell Stem Unit, Department of Translational Research, National Cancer Center CRO-IRCSS, 33081, Aviano, Italy
| | - Paolo Bonaldo
- Department of Molecular Medicine, University of Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy. .,CRIBI Biotechnology Center, University of Padova, 35131, Padova, Italy.
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23
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Christen F, Hablesreiter R, Hoyer K, Hennch C, Maluck-Böttcher A, Segler A, Madadi A, Frick M, Bullinger L, Briest F, Damm F. Modeling clonal hematopoiesis in umbilical cord blood cells by CRISPR/Cas9. Leukemia 2022; 36:1102-1110. [PMID: 34782715 PMCID: PMC8979818 DOI: 10.1038/s41375-021-01469-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 12/17/2022]
Abstract
To investigate clonal hematopoiesis associated gene mutations in vitro and to unravel the direct impact on the human stem and progenitor cell (HSPC) compartment, we targeted healthy, young hematopoietic progenitor cells, derived from umbilical cord blood samples, with CRISPR/Cas9 technology. Site-specific mutations were introduced in defined regions of DNMT3A, TET2, and ASXL1 in CD34+ progenitor cells that were subsequently analyzed in short-term as well as long-term in vitro culture assays to assess self-renewal and differentiation capacities. Colony-forming unit (CFU) assays revealed enhanced self-renewal of TET2 mutated (TET2mut) cells, whereas ASXL1mut as well as DNMT3Amut cells did not reveal significant changes in short-term culture. Strikingly, enhanced colony formation could be detected in long-term culture experiments in all mutants, indicating increased self-renewal capacities. While we could also demonstrate preferential clonal expansion of distinct cell clones for all mutants, the clonal composition after long-term culture revealed a mutation-specific impact on HSPCs. Thus, by using primary umbilical cord blood cells, we were able to investigate epigenetic driver mutations without confounding factors like age or a complex mutational landscape, and our findings provide evidence for a direct impact of clonal hematopoiesis-associated mutations on self-renewal and clonal composition of human stem and progenitor cells.
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Affiliation(s)
- Friederike Christen
- grid.7468.d0000 0001 2248 7639Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology, and Cancer Immunology, Berlin, Germany
| | - Raphael Hablesreiter
- grid.7468.d0000 0001 2248 7639Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology, and Cancer Immunology, Berlin, Germany
| | - Kaja Hoyer
- grid.7468.d0000 0001 2248 7639Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology, and Cancer Immunology, Berlin, Germany
| | - Cornelius Hennch
- grid.7468.d0000 0001 2248 7639Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology, and Cancer Immunology, Berlin, Germany
| | - Antje Maluck-Böttcher
- grid.7468.d0000 0001 2248 7639Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology, and Cancer Immunology, Berlin, Germany
| | - Angela Segler
- grid.7468.d0000 0001 2248 7639Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Gynecology with Center for Oncological Surgery, Berlin, Germany ,grid.7468.d0000 0001 2248 7639Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Obstetrics, Berlin, Germany
| | - Annett Madadi
- grid.7468.d0000 0001 2248 7639Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Obstetrics, Berlin, Germany
| | - Mareike Frick
- grid.7468.d0000 0001 2248 7639Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology, and Cancer Immunology, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lars Bullinger
- grid.7468.d0000 0001 2248 7639Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology, and Cancer Immunology, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Franziska Briest
- grid.7468.d0000 0001 2248 7639Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology, and Cancer Immunology, Berlin, Germany
| | - Frederik Damm
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Hematology, Oncology, and Cancer Immunology, Berlin, Germany. .,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.
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24
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Guo P, Farahat AA, Paul A, Boykin DW, Wilson WD. Engineered modular heterocyclic-diamidines for sequence-specific recognition of mixed AT/GC base pairs at the DNA minor groove. Chem Sci 2021; 12:15849-15861. [PMID: 35024109 PMCID: PMC8672716 DOI: 10.1039/d1sc04720e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/28/2021] [Indexed: 12/20/2022] Open
Abstract
This report describes a breakthrough in a project to design minor groove binders to recognize any sequence of DNA. A key goal is to invent synthetic chemistry for compound preparation to recognize an adjacent GG sequence that has been difficult to target. After trying several unsuccessful compound designs, an N-alkyl-benzodiimidazole structure was selected to provide two H-bond acceptors for the adjacent GG-NH groups. Flanking thiophenes provide a preorganized structure with strong affinity, DB2831, and the structure is terminated by phenyl-amidines. The binding experimental results for DB2831 with a target AAAGGTTT sequence were successful and include a high ΔT m, biosensor SPR with a K D of 4 nM, a similar K D from fluorescence titrations and supporting competition mass spectrometry. MD analysis of DB2831 bound to an AAAGGTTT site reveals that the two unprotonated N of the benzodiimidazole group form strong H-bonds (based on distance) with the two central G-NH while the central -CH of the benzodiimidazole is close to the -C[double bond, length as m-dash]O of a C base. These three interactions account for the strong preference of DB2831 for a -GG- sequence. Surprisingly, a complex with one dynamic, interfacial water is favored with 75% occupancy.
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Affiliation(s)
- Pu Guo
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
| | - Abdelbasset A Farahat
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University Mansoura 35516 Egypt
| | - Ananya Paul
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
| | - David W Boykin
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
| | - W David Wilson
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
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25
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Dang D, Liu Y, Zhou Q, Li H, Wang Y, Wu H. Identification of a novel IRF8 homozygous mutation causing neutrophilia, monocytopenia and fatal infection in a female neonate. INFECTION GENETICS AND EVOLUTION 2021; 96:105121. [PMID: 34666172 DOI: 10.1016/j.meegid.2021.105121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/12/2021] [Accepted: 10/11/2021] [Indexed: 12/29/2022]
Abstract
Inborn errors of immunity (IEIs) result from mutations in genes involved in host immune defense and immune regulation. Herein, we report the identification of a novel IRF8 mutation in a neonate with an IEI. DNA samples from both the neonate and her parents were subjected to DNA sequencing, and the immune status of the patient was assessed. We identified a mutation (c.331C > T, p. Arg111*) in the interferon regulatory factor 8 (IRF8) gene that manifested as sever dysfunctional neutrophilia (96.53 × 109/l) and monocytopenia (0.02 × 109/l). The patient's CD3+ T cell and CD8+ T cell counts were decreased. Her levels of IFN-γ were low even during severe infection. The mRNA expression levels of IRF8 were lower than normal. Her clinical manifestations included a recurrent and progressively fatal infection. Since IRF8 plays a key role in the differentiation and development of immune cells, we suspected that the novel mutation (c.331C > T, p. Arg111*) may be consistent with a severe loss of IRF8 function and result in a failure of immune cells to differentiate and maturation, and lead to a severe infection with early onset.
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Affiliation(s)
- Dan Dang
- Department of Neonatology, First Hospital of Jilin University, Changchun 130021, China
| | - Ying Liu
- Department of Neonatology, First Hospital of Jilin University, Changchun 130021, China
| | - Qi Zhou
- Department of Neonatology, First Hospital of Jilin University, Changchun 130021, China
| | - Heng Li
- Department of Neonatology, First Hospital of Jilin University, Changchun 130021, China
| | - Ying Wang
- Research Institute of pediatrics, First Hospital of Jilin University, Changchun 130021, China
| | - Hui Wu
- Department of Neonatology, First Hospital of Jilin University, Changchun 130021, China.
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26
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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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27
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Gluba-Brzózka A, Franczyk B, Rysz-Górzyńska M, Rokicki R, Koziarska-Rościszewska M, Rysz J. Pathomechanisms of Immunological Disturbances in β-Thalassemia. Int J Mol Sci 2021; 22:ijms22189677. [PMID: 34575839 PMCID: PMC8469188 DOI: 10.3390/ijms22189677] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/25/2021] [Accepted: 08/25/2021] [Indexed: 01/19/2023] Open
Abstract
Thalassemia, a chronic disease with chronic anemia, is caused by mutations in the β-globin gene, leading to reduced levels or complete deficiency of β-globin chain synthesis. Patients with β-thalassemia display variable clinical severity which ranges from asymptomatic features to severe transfusion-dependent anemia and complications in multiple organs. They not only are at increased risk of blood-borne infections resulting from multiple transfusions, but they also show enhanced susceptibility to infections as a consequence of coexistent immune deficiency. Enhanced susceptibility to infections in β-thalassemia patients is associated with the interplay of several complex biological processes. β-thalassemia-related abnormalities of the innate immune system include decreased levels of complement, properdin, and lysozyme, reduced absorption and phagocytic ability of polymorphonuclear neutrophils, disturbed chemotaxis, and altered intracellular metabolism processes. According to available literature data, immunological abnormalities observed in patients with thalassemia can be caused by both the disease itself as well as therapies. The most important factors promoting such alterations involve iron overload, phenotypical and functional abnormalities of immune system cells resulting from chronic inflammation oxidative stress, multiple blood transfusion, iron chelation therapy, and splenectomy. Unravelling the mechanisms underlying immune deficiency in β-thalassemia patients may enable the designing of appropriate therapies for this group of patients.
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Affiliation(s)
- Anna Gluba-Brzózka
- Department of Nephrology, Hypertension and Family Medicine, Medical University of Lodz, 90-549 Lodz, Poland; (B.F.); (M.K.-R.); (J.R.)
- Correspondence: or ; Tel.: +48-42-639-3750
| | - Beata Franczyk
- Department of Nephrology, Hypertension and Family Medicine, Medical University of Lodz, 90-549 Lodz, Poland; (B.F.); (M.K.-R.); (J.R.)
| | - Magdalena Rysz-Górzyńska
- Department of Ophthalmology and Visual Rehabilitation, Medical University of Lodz, 90-549 Lodz, Poland;
| | - Robert Rokicki
- Clinic of Hand Surgery, Medical University of Lodz, 90-549 Lodz, Poland;
| | - Małgorzata Koziarska-Rościszewska
- Department of Nephrology, Hypertension and Family Medicine, Medical University of Lodz, 90-549 Lodz, Poland; (B.F.); (M.K.-R.); (J.R.)
| | - Jacek Rysz
- Department of Nephrology, Hypertension and Family Medicine, Medical University of Lodz, 90-549 Lodz, Poland; (B.F.); (M.K.-R.); (J.R.)
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28
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Taylor SJ, Sundaravel S, Steidl U. Exploiting a key transcriptional dependency: ZMYND8 and IRF8 in AML. Mol Cell 2021; 81:3445-3446. [PMID: 34478652 DOI: 10.1016/j.molcel.2021.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
In this issue of Molecular Cell, Cao et al. (2021) report that AML cells are specifically addicted to an IRF8-MEF2D gene expression network. Furthermore, they identify a chromatin reader, ZMYND8, as the upstream regulator of the IRF8-MEF2D program whose activity is critical for AML cell survival.
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Affiliation(s)
- Samuel J Taylor
- Departments of Cell Biology, and of Medicine, Blood Cancer Institute, Albert Einstein Cancer Center; and Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Sriram Sundaravel
- Departments of Cell Biology, and of Medicine, Blood Cancer Institute, Albert Einstein Cancer Center; and Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Ulrich Steidl
- Departments of Cell Biology, and of Medicine, Blood Cancer Institute, Albert Einstein Cancer Center; and Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.
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29
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Barabino SML, Citterio E, Ronchi AE. Transcription Factors, R-Loops and Deubiquitinating Enzymes: Emerging Targets in Myelodysplastic Syndromes and Acute Myeloid Leukemia. Cancers (Basel) 2021; 13:cancers13153753. [PMID: 34359655 PMCID: PMC8345071 DOI: 10.3390/cancers13153753] [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: 06/16/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary The advent of DNA massive sequencing technologies has allowed for the first time an extensive look into the heterogeneous spectrum of genes and mutations underpinning myelodysplastic syndromes (MDSs) and acute myeloid leukemia (AML). In this review, we wish to explore the most recent advances and the rationale for the potential therapeutic interest of three main actors in myelo-leukemic transformation: transcription factors that govern myeloid differentiation; RNA splicing factors, which ensure proper mRNA maturation and whose mutations increase R-loops formation; and deubiquitinating enzymes, which contribute to genome stability in hematopoietic stem cells (HSCs). Abstract Myeloid neoplasms encompass a very heterogeneous family of diseases characterized by the failure of the molecular mechanisms that ensure a balanced equilibrium between hematopoietic stem cells (HSCs) self-renewal and the proper production of differentiated cells. The origin of the driver mutations leading to preleukemia can be traced back to HSC/progenitor cells. Many properties typical to normal HSCs are exploited by leukemic stem cells (LSCs) to their advantage, leading to the emergence of a clonal population that can eventually progress to leukemia with variable latency and evolution. In fact, different subclones might in turn develop from the original malignant clone through accumulation of additional mutations, increasing their competitive fitness. This process ultimately leads to a complex cancer architecture where a mosaic of cellular clones—each carrying a unique set of mutations—coexists. The repertoire of genes whose mutations contribute to the progression toward leukemogenesis is broad. It encompasses genes involved in different cellular processes, including transcriptional regulation, epigenetics (DNA and histones modifications), DNA damage signaling and repair, chromosome segregation and replication (cohesin complex), RNA splicing, and signal transduction. Among these many players, transcription factors, RNA splicing proteins, and deubiquitinating enzymes are emerging as potential targets for therapeutic intervention.
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30
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Preleukemic and leukemic evolution at the stem cell level. Blood 2021; 137:1013-1018. [PMID: 33275656 DOI: 10.1182/blood.2019004397] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023] Open
Abstract
Hematological malignancies are an aggregate of diverse populations of cells that arise following a complex process of clonal evolution and selection. Recent approaches have facilitated the study of clonal populations and their evolution over time across multiple phenotypic cell populations. In this review, we present current concepts on the role of clonal evolution in leukemic initiation, disease progression, and relapse. We highlight recent advances and unanswered questions about the contribution of the hematopoietic stem cell population to these processes.
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31
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Gene Expression at a Single Molecule Level: Implications for MDS and AML. Blood 2021; 138:625-636. [PMID: 34157070 DOI: 10.1182/blood.2019004261] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022] Open
Abstract
Non-genetic heterogeneity, or gene expression stochasticity, is an important source of variability in biological systems. With the advent and improvement of single molecule resolution technologies, it has been shown that transcription dynamics and resultant transcript number fluctuations generate significant cell-to-cell variability that has important biological effects and may contribute substantially to both tissue homeostasis and disease. In this respect, the pathophysiology of stem cell-derived malignancies such as AML and MDS, which has historically been studied at the ensemble level, may require re-evaluation. To that end, it is our aim in this review to highlight the results of recent single-molecule, biophysical, and systems studies of gene expression dynamics, with the explicit purpose of demonstrating how the insights from these basic science studies may help inform and progress the field of leukemia biology and, ultimately, research into novel therapies.
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32
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Harama D, Yahata T, Kagami K, Abe M, Ando N, Kasai S, Tamai M, Akahane K, Inukai T, Kiyokawa N, Ibrahim AA, Ando K, Sugita K. IMiDs uniquely synergize with TKIs to upregulate apoptosis of Philadelphia chromosome-positive acute lymphoblastic leukemia cells expressing a dominant-negative IKZF1 isoform. Cell Death Discov 2021; 7:139. [PMID: 34117218 PMCID: PMC8195985 DOI: 10.1038/s41420-021-00523-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 05/01/2021] [Indexed: 11/24/2022] Open
Abstract
The long-term prognosis of Philadelphia chromosome-positive acute lymphoblastic leukemia (Ph + ALL) is still unsatisfactory even after the emergence of tyrosine kinase inhibitors (TKIs) against chimeric BCR-ABL, and this is associated with the high incidence of genetic alterations of Ikaros family zinc finger 1 (IKZF1), most frequently the hemi-allelic loss of exons 4–7 expressing a dominant-negative isoform Ik6. We found that lenalidomide (LEN), a representative of immunomodulatory drugs (IMiDs), which have been long used for the treatment of multiple myeloma, specifically induced accumulation of Ik6 with the disappearance of functional isoforms within 24 h (i.e., abrupt and complete shut-down of the IKZF1 activity) in Ik6-positive Ph+ALL cells in a neddylation-dependent manner. The functional IKZF3 isoforms expression was also abruptly and markedly downregulated. The LEN treatment specifically suppressed proliferation of Ik6-positive-Ph+ALL cells by inducing cell cycle arrest via downregulation of cyclins D3 and E and CDK2, and of importance, markedly upregulated their apoptosis in synergy with the TKI imatinib (IM). Apoptosis of IM-resistant Ph+ALL cells with T315I mutation of BCR-ABL was also upregulated by LEN in the presence of the newly developed TKI ponatinib. Analyses of flow cytometry, western blot, and oligonucleotide array revealed that apoptosis was caspase-/p53-dependent and associated with upregulation of pro-apoptotic Bax/Bim, enhanced dephosphorylation of BCR-ABL/Akt, and downregulation of oncogenic helicase genes HILLS, CDC6, and MCMs4 and 8. Further, the synergism of LEN with IM was clearly documented as a significant prolongation of survival in the xenograft mice model. Because this synergism was further potentiated in vitro by dexamethasone, a key drug for ALL treatment, the strategy of repositioning IMiDs for the treatment of Ik6-positive Ph+ALL patients certainly shed new light on an outpatient-based treatment option for achieving their long-term durable remission and higher QOL, particularly for those who are not tolerable to intensified therapeutic approaches.
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Affiliation(s)
- Daisuke Harama
- Department of Pediatrics, Graduate School of Medicine, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Takashi Yahata
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Keiko Kagami
- Department of Pediatrics, Graduate School of Medicine, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Masako Abe
- Department of Pediatrics, Graduate School of Medicine, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Norie Ando
- Department of Pediatrics, Graduate School of Medicine, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Shin Kasai
- Department of Pediatrics, Graduate School of Medicine, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Minori Tamai
- Department of Pediatrics, Graduate School of Medicine, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Koshi Akahane
- Department of Pediatrics, Graduate School of Medicine, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Takeshi Inukai
- Department of Pediatrics, Graduate School of Medicine, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Nobutaka Kiyokawa
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Abd Aziz Ibrahim
- Department of Hematology and Oncology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Kiyoshi Ando
- Department of Hematology and Oncology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Kanji Sugita
- Department of Pediatrics, Graduate School of Medicine, University of Yamanashi, Chuo, Yamanashi, Japan.
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33
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O'Brien G, Cruz-Garcia L, Zyla J, Brown N, Finnon R, Polanska J, Badie C. Kras mutations and PU.1 promoter methylation are new pathways in murine radiation-induced AML. Carcinogenesis 2021; 41:1104-1112. [PMID: 31646336 PMCID: PMC7422620 DOI: 10.1093/carcin/bgz175] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 09/17/2019] [Accepted: 10/21/2019] [Indexed: 12/16/2022] Open
Abstract
Therapy-related and more specifically radiotherapy-associated acute myeloid leukaemia (AML) is a well-recognized potential complication of cytotoxic therapy for the treatment of a primary cancer. The CBA mouse model is used to study radiation leukaemogenesis mechanisms with Sfpi1/PU.1 deletion and point mutation already identified as driving events during AML development. To identify new pathways, we analysed 123 mouse radiation-induced AML (rAML) samples for the presence of mutations identified previously in human AML and found three genes to be mutated; Sfpi1 R235 (68%), Flt3-ITD (4%) and Kras G12 (3%), of which G12R was previously unreported. Importantly, a significant decrease in Sfpi1 gene expression is found almost exclusively in rAML samples without an Sfpi1 R235 mutation and is specifically associated with up-regulation of mir-1983 and mir-582-5p. Moreover, this down-regulation of Sfpi1 mRNA is negatively correlated with DNA methylation levels at specific CpG sites upstream of the Sfpi1 transcriptional start site. The down regulation of Sfpi1/PU.1 has also been reported in human AML cases revealing one common pathway of myeloid disruption between mouse and human AML where dysregulation of Sfpi1/PU.1 is a necessary step in AML development.
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Affiliation(s)
- Gráinne O'Brien
- Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Oxfordshire, UK
| | - Lourdes Cruz-Garcia
- Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Oxfordshire, UK
| | - Joanna Zyla
- Silesian University of Technology, Data Mining Division, Gliwice, Poland
| | - Natalie Brown
- Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Oxfordshire, UK
| | - Rosemary Finnon
- Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Oxfordshire, UK
| | - Joanna Polanska
- Silesian University of Technology, Data Mining Division, Gliwice, Poland
| | - Christophe Badie
- Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Oxfordshire, UK
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Fiskus W, Mill CP, Nabet B, Perera D, Birdwell C, Manshouri T, Lara B, Kadia TM, DiNardo C, Takahashi K, Daver N, Bose P, Masarova L, Pemmaraju N, Kornblau S, Borthakur G, Montalban-Bravo G, Manero GG, Sharma S, Stubbs M, Su X, Green MR, Coarfa C, Verstovsek S, Khoury JD, Vakoc CR, Bhalla KN. Superior efficacy of co-targeting GFI1/KDM1A and BRD4 against AML and post-MPN secondary AML cells. Blood Cancer J 2021; 11:98. [PMID: 34016956 PMCID: PMC8138012 DOI: 10.1038/s41408-021-00487-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/20/2021] [Accepted: 04/30/2021] [Indexed: 12/15/2022] Open
Abstract
There is an unmet need to overcome nongenetic therapy-resistance to improve outcomes in AML, especially post-myeloproliferative neoplasm (MPN) secondary (s) AML. Studies presented describe effects of genetic knockout, degradation or small molecule targeted-inhibition of GFI1/LSD1 on active enhancers, altering gene-expressions and inducing differentiation and lethality in AML and (MPN) sAML cells. A protein domain-focused CRISPR screen in LSD1 (KDM1A) inhibitor (i) treated AML cells, identified BRD4, MOZ, HDAC3 and DOT1L among the codependencies. Our findings demonstrate that co-targeting LSD1 and one of these co-dependencies exerted synergistic in vitro lethality in AML and post-MPN sAML cells. Co-treatment with LSD1i and the JAKi ruxolitinib was also synergistically lethal against post-MPN sAML cells. LSD1i pre-treatment induced GFI1, PU.1 and CEBPα but depleted c-Myc, overcoming nongenetic resistance to ruxolitinib, or to BETi in post-MPN sAML cells. Co-treatment with LSD1i and BETi or ruxolitinib exerted superior in vivo efficacy against post-MPN sAML cells. These findings highlight LSD1i-based combinations that merit testing for clinical efficacy, especially to overcome nongenetic therapy-resistance in AML and post-MPN sAML.
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Affiliation(s)
- Warren Fiskus
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | | | - Behnam Nabet
- Department of Cancer Biology, Dana-Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Dimuthu Perera
- Department of Molecular and Cellular Biology Baylor College of Medicine, Houston, TX, USA
| | | | - Taghi Manshouri
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Bernardo Lara
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Tapan M Kadia
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Courtney DiNardo
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Koichi Takahashi
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Naval Daver
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Prithviraj Bose
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Lucia Masarova
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Naveen Pemmaraju
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Steven Kornblau
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Gautam Borthakur
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | | | | | - Sunil Sharma
- The Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | | | - Xiaoping Su
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Michael R Green
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology Baylor College of Medicine, Houston, TX, USA
| | - Srdan Verstovsek
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Joseph D Khoury
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | | | - Kapil N Bhalla
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA.
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35
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Abstract
In this issue, Le Coz et al. (2021. J. Exp. Med.https://doi.org/10.1084/jem.20201750) describe a novel immunodeficiency syndrome caused by mutations in SPI1. Through a series of in-depth studies, the authors provide insights into how SPI1 affects blood lineage specification, highlighting the important role of master transcription factors as cellular fate determinants.
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Affiliation(s)
- Lara Wahlster
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA.,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA.,Broad Institute of MIT and Harvard, Cambridge, MA
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36
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Le Coz C, Nguyen DN, Su C, Nolan BE, Albrecht AV, Xhani S, Sun D, Demaree B, Pillarisetti P, Khanna C, Wright F, Chen PA, Yoon S, Stiegler AL, Maurer K, Garifallou JP, Rymaszewski A, Kroft SH, Olson TS, Seif AE, Wertheim G, Grant SFA, Vo LT, Puck JM, Sullivan KE, Routes JM, Zakharova V, Shcherbina A, Mukhina A, Rudy NL, Hurst ACE, Atkinson TP, Boggon TJ, Hakonarson H, Abate AR, Hajjar J, Nicholas SK, Lupski JR, Verbsky J, Chinn IK, Gonzalez MV, Wells AD, Marson A, Poon GMK, Romberg N. Constrained chromatin accessibility in PU.1-mutated agammaglobulinemia patients. J Exp Med 2021; 218:212070. [PMID: 33951726 PMCID: PMC8105723 DOI: 10.1084/jem.20201750] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 02/09/2021] [Accepted: 03/16/2021] [Indexed: 12/19/2022] Open
Abstract
The pioneer transcription factor (TF) PU.1 controls hematopoietic cell fate by decompacting stem cell heterochromatin and allowing nonpioneer TFs to enter otherwise inaccessible genomic sites. PU.1 deficiency fatally arrests lymphopoiesis and myelopoiesis in mice, but human congenital PU.1 disorders have not previously been described. We studied six unrelated agammaglobulinemic patients, each harboring a heterozygous mutation (four de novo, two unphased) of SPI1, the gene encoding PU.1. Affected patients lacked circulating B cells and possessed few conventional dendritic cells. Introducing disease-similar SPI1 mutations into human hematopoietic stem and progenitor cells impaired early in vitro B cell and myeloid cell differentiation. Patient SPI1 mutations encoded destabilized PU.1 proteins unable to nuclear localize or bind target DNA. In PU.1-haploinsufficient pro–B cell lines, euchromatin was less accessible to nonpioneer TFs critical for B cell development, and gene expression patterns associated with the pro– to pre–B cell transition were undermined. Our findings molecularly describe a novel form of agammaglobulinemia and underscore PU.1’s critical, dose-dependent role as a hematopoietic euchromatin gatekeeper.
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Affiliation(s)
- Carole Le Coz
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA
| | - David N Nguyen
- Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA.,Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA.,Diabetes Center, University of California San Francisco, San Francisco, CA.,Innovative Genomics Institute, University of California Berkeley, Berkeley, CA.,Gladstone-University of California San Francisco Institute of Genomic Immunology, San Francisco, CA
| | - Chun Su
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA.,Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Brian E Nolan
- Division of Rheumatology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL.,Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Amanda V Albrecht
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA
| | - Suela Xhani
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA
| | - Di Sun
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Benjamin Demaree
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA.,University of California Berkeley-University of California San Francisco Graduate Program in Bioengineering, University of California, San Francisco, CA
| | - Piyush Pillarisetti
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Caroline Khanna
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Francis Wright
- Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA.,Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA
| | - Peixin Amy Chen
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA.,Diabetes Center, University of California San Francisco, San Francisco, CA.,Innovative Genomics Institute, University of California Berkeley, Berkeley, CA.,Gladstone-University of California San Francisco Institute of Genomic Immunology, San Francisco, CA
| | - Samuel Yoon
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Amy L Stiegler
- Departments of Pharmacology, Yale University, New Haven, CT
| | - Kelly Maurer
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA
| | - James P Garifallou
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Amy Rymaszewski
- Division of Allergy and Immunology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
| | - Steven H Kroft
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI
| | - Timothy S Olson
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA
| | - Alix E Seif
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA
| | - Gerald Wertheim
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Struan F A Grant
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA.,Division of Diabetes and Endocrinology, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Linda T Vo
- Diabetes Center, University of California San Francisco, San Francisco, CA.,Innovative Genomics Institute, University of California Berkeley, Berkeley, CA
| | - Jennifer M Puck
- Division of Allergy, Immunology, and Bone Marrow Transplantation, Department of Pediatrics, University of California, San Francisco, CA.,University of California San Francsico Institute for Human Genetics and Smith Cardiovascular Research Institute, University of California, San Francisco, CA.,UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Kathleen E Sullivan
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - John M Routes
- Division of Allergy and Immunology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
| | - Viktoria Zakharova
- Laboratory of Molecular Biology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Anna Shcherbina
- Department of Immunology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Anna Mukhina
- Department of Immunology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Natasha L Rudy
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL.,Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL
| | - T Prescott Atkinson
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL
| | - Titus J Boggon
- Departments of Pharmacology, Yale University, New Haven, CT.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA.,University of California Berkeley-University of California San Francisco Graduate Program in Bioengineering, University of California, San Francisco, CA.,Chan Zuckerberg Biohub, San Francisco, CA
| | - Joud Hajjar
- William T. Shearer Center for Human Immunobiology, Texas Children's Hospital, Houston, TX.,Department of Immunology, Allergy and Rheumatology, Baylor College of Medicine, Houston, TX
| | - Sarah K Nicholas
- William T. Shearer Center for Human Immunobiology, Texas Children's Hospital, Houston, TX.,Department of Immunology, Allergy and Rheumatology, Baylor College of Medicine, Houston, TX
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX.,Texas Children's Hospital, Houston, TX.,Baylor-Hopkins Center for Mendelian Genomics, Houston, TX
| | - James Verbsky
- Division of Allergy and Immunology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
| | - Ivan K Chinn
- William T. Shearer Center for Human Immunobiology, Texas Children's Hospital, Houston, TX.,Department of Immunology, Allergy and Rheumatology, Baylor College of Medicine, Houston, TX
| | - Michael V Gonzalez
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Alex Marson
- Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA.,Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA.,Diabetes Center, University of California San Francisco, San Francisco, CA.,Innovative Genomics Institute, University of California Berkeley, Berkeley, CA.,Gladstone-University of California San Francisco Institute of Genomic Immunology, San Francisco, CA.,Chan Zuckerberg Biohub, San Francisco, CA.,Parker Institute for Cancer Immunotherapy, San Francisco, CA
| | - Gregory M K Poon
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA
| | - Neil Romberg
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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37
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Chavez JS, Rabe JL, Loeffler D, Higa KC, Hernandez G, Mills TS, Ahmed N, Gessner RL, Ke Z, Idler BM, Niño KE, Kim H, Myers JR, Stevens BM, Davizon-Castillo P, Jordan CT, Nakajima H, Ashton J, Welner RS, Schroeder T, DeGregori J, Pietras EM. PU.1 enforces quiescence and limits hematopoietic stem cell expansion during inflammatory stress. J Exp Med 2021; 218:211996. [PMID: 33857288 PMCID: PMC8056754 DOI: 10.1084/jem.20201169] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 02/01/2021] [Accepted: 03/17/2021] [Indexed: 12/27/2022] Open
Abstract
Hematopoietic stem cells (HSCs) are capable of entering the cell cycle to replenish the blood system in response to inflammatory cues; however, excessive proliferation in response to chronic inflammation can lead to either HSC attrition or expansion. The mechanism(s) that limit HSC proliferation and expansion triggered by inflammatory signals are poorly defined. Here, we show that long-term HSCs (HSCLT) rapidly repress protein synthesis and cell cycle genes following treatment with the proinflammatory cytokine interleukin (IL)-1. This gene program is associated with activation of the transcription factor PU.1 and direct PU.1 binding at repressed target genes. Notably, PU.1 is required to repress cell cycle and protein synthesis genes, and IL-1 exposure triggers aberrant protein synthesis and cell cycle activity in PU.1-deficient HSCs. These features are associated with expansion of phenotypic PU.1-deficient HSCs. Thus, we identify a PU.1-dependent mechanism triggered by innate immune stimulation that limits HSC proliferation and pool size. These findings provide insight into how HSCs maintain homeostasis during inflammatory stress.
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Affiliation(s)
- James S Chavez
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Jennifer L Rabe
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Dirk Loeffler
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zurich, Basel, Switzerland
| | - Kelly C Higa
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Giovanny Hernandez
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Taylor S Mills
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO.,Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Nouraiz Ahmed
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zurich, Basel, Switzerland
| | - Rachel L Gessner
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Zhonghe Ke
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Beau M Idler
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Katia E Niño
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Hyunmin Kim
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Jason R Myers
- Genomics Research Center, University of Rochester, Rochester, NY
| | - Brett M Stevens
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | | | - Craig T Jordan
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Hideaki Nakajima
- Department of Stem Cell and Immune Regulation, Yokohama City University School of Medicine, Yokohama, Japan
| | - John Ashton
- Genomics Research Center, University of Rochester, Rochester, NY
| | - Robert S Welner
- Division of Hematology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Timm Schroeder
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zurich, Basel, Switzerland
| | - James DeGregori
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO.,Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO.,Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO.,Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Eric M Pietras
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO.,Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO
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38
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Schwenger E, Steidl U. An evolutionary approach to clonally complex hematologic disorders. Blood Cancer Discov 2021; 2:201-215. [PMID: 34027415 DOI: 10.1158/2643-3230.bcd-20-0219] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Emerging clonal complexity has brought into question the way in which we perceive and, in turn, treat disorders of the hematopoietic system. Former models of cell-intrinsic clonal dominance driven by acquisition of driver genes in a stereotypic sequence are often insufficient in explaining observations such as clonal hematopoiesis, and new paradigms are in order. Here, we review the evidence both within the hematologic malignancy field and also borrow from perspectives rooted in evolutionary biology to reframe pathogenesis of hematologic disorders as dynamic processes involving complex interplays of genetic and non-genetic subclones and the tissue microenvironment in which they reside.
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Affiliation(s)
- Emily Schwenger
- Albert Einstein College of Medicine - Montefiore Health System, Bronx, NY, U.S.A
| | - Ulrich Steidl
- Departments of Cell Biology, and Medicine (Oncology), Blood Cancer Institute, Albert Einstein Cancer Center, Gottesman Institute for Stem Cell Research and Regenerative Medicine
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39
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Ueda K, Kumari R, Schwenger E, Wheat JC, Bohorquez O, Narayanagari SR, Taylor SJ, Carvajal LA, Pradhan K, Bartholdy B, Todorova TI, Goto H, Sun D, Chen J, Shan J, Song Y, Montagna C, Xiong S, Lozano G, Pellagatti A, Boultwood J, Verma A, Steidl U. MDMX acts as a pervasive preleukemic-to-acute myeloid leukemia transition mechanism. Cancer Cell 2021; 39:529-547.e7. [PMID: 33667384 PMCID: PMC8575661 DOI: 10.1016/j.ccell.2021.02.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 11/23/2020] [Accepted: 02/08/2021] [Indexed: 12/17/2022]
Abstract
MDMX is overexpressed in the vast majority of patients with acute myeloid leukemia (AML). We report that MDMX overexpression increases preleukemic stem cell (pre-LSC) number and competitive advantage. Utilizing five newly generated murine models, we found that MDMX overexpression triggers progression of multiple chronic/asymptomatic preleukemic conditions to overt AML. Transcriptomic and proteomic studies revealed that MDMX overexpression exerts this function, unexpectedly, through activation of Wnt/β-Catenin signaling in pre-LSCs. Mechanistically, MDMX binds CK1α and leads to accumulation of β-Catenin in a p53-independent manner. Wnt/β-Catenin inhibitors reverse MDMX-induced pre-LSC properties, and synergize with MDMX-p53 inhibitors. Wnt/β-Catenin signaling correlates with MDMX expression in patients with preleukemic myelodysplastic syndromes and is associated with increased risk of progression to AML. Our work identifies MDMX overexpression as a pervasive preleukemic-to-AML transition mechanism in different genetically driven disease subtypes, and reveals Wnt/β-Catenin as a non-canonical MDMX-driven pathway with therapeutic potential for progression prevention and cancer interception.
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Affiliation(s)
- Koki Ueda
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Rajni Kumari
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Emily Schwenger
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Justin C Wheat
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Oliver Bohorquez
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Swathi-Rao Narayanagari
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Stem Cell Isolation and Xenotransplantation Facility, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Samuel J Taylor
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Luis A Carvajal
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Kith Pradhan
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Boris Bartholdy
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Tihomira I Todorova
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Hiroki Goto
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Daqian Sun
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Stem Cell Isolation and Xenotransplantation Facility, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jiahao Chen
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jidong Shan
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Yinghui Song
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Cristina Montagna
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Shunbin Xiong
- Department of Genetics, Division of Basic Science Research, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guillermina Lozano
- Department of Genetics, Division of Basic Science Research, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Andrea Pellagatti
- Blood Cancer UK Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, and NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford OX3 9DU, UK
| | - Jacqueline Boultwood
- Blood Cancer UK Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, and NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford OX3 9DU, UK
| | - Amit Verma
- Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Division of Hemato-Oncology, Department of Medicine (Oncology), Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY 10461, USA; Blood Cancer Institute, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY 10461, USA; Albert Einstein Cancer Center, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY 10461, USA
| | - Ulrich Steidl
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Division of Hemato-Oncology, Department of Medicine (Oncology), Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY 10461, USA; Blood Cancer Institute, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY 10461, USA; Albert Einstein Cancer Center, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY 10461, USA.
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40
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Wang X, Jin P, Zhang Y, Wang K. CircSPI1 acts as an oncogene in acute myeloid leukemia through antagonizing SPI1 and interacting with microRNAs. Cell Death Dis 2021; 12:297. [PMID: 33741901 PMCID: PMC7979773 DOI: 10.1038/s41419-021-03566-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 02/07/2023]
Abstract
PU.1 (encoded by SPI1) is essential for myeloid development, and inhibition of its expression and activity can lead to acute myeloid leukemia (AML). The precise regulation of PU.1 expression is crucial for the development of AML, and the discovery of circular RNAs (circRNAs) can add a new layer of information on regulation. Here, we found that circSPI1, the circular RNA derived from the SPI1 gene, is highly expressed in AML but not in normal counterparts. Unlike SPI1, a tumor suppressor and being lowly expressed in AML, we demonstrate that circSPI1 acts as an oncogene, evidenced by the observation that circSPI1 knockdown induces myeloid differentiation and apoptosis of AML cells. We provide mechanistic evidence for multiple regulatory roles of circSPI1 in AML progression. On one hand, circSPI1 contributes to myeloid differentiation of AML cells by interacting with the translation initiation factor eIF4AIII to antagonize PU.1 expression at the translation level. On the other hand, circSPI1 contributes to proliferation and apoptosis by interacting with miR-1307-3p, miR-382-5p, and miR-767-5p; this role is uncoupled with SPI1. Finally, we illustrate the clinical significance of circSPI1 by showing that circSPI1-regulated genes are associated with the clinical outcome of AML patients. Our data provide new insight into the complex SPI1 gene regulation now involving circSPI1.
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Affiliation(s)
- Xiaoling Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Peng Jin
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Kankan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China. .,Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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41
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Giacopelli B, Wang M, Cleary A, Wu YZ, Schultz AR, Schmutz M, Blachly JS, Eisfeld AK, Mundy-Bosse B, Vosberg S, Greif PA, Claus R, Bullinger L, Garzon R, Coombes KR, Bloomfield CD, Druker BJ, Tyner JW, Byrd JC, Oakes CC. DNA methylation epitypes highlight underlying developmental and disease pathways in acute myeloid leukemia. Genome Res 2021; 31:747-761. [PMID: 33707228 PMCID: PMC8092005 DOI: 10.1101/gr.269233.120] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 03/09/2021] [Indexed: 02/06/2023]
Abstract
Acute myeloid leukemia (AML) is a molecularly complex disease characterized by heterogeneous tumor genetic profiles and involving numerous pathogenic mechanisms and pathways. Integration of molecular data types across multiple patient cohorts may advance current genetic approaches for improved subclassification and understanding of the biology of the disease. Here, we analyzed genome-wide DNA methylation in 649 AML patients using Illumina arrays and identified a configuration of 13 subtypes (termed “epitypes”) using unbiased clustering. Integration of genetic data revealed that most epitypes were associated with a certain recurrent mutation (or combination) in a majority of patients, yet other epitypes were largely independent. Epitypes showed developmental blockage at discrete stages of myeloid differentiation, revealing epitypes that retain arrested hematopoietic stem-cell-like phenotypes. Detailed analyses of DNA methylation patterns identified unique patterns of aberrant hyper- and hypomethylation among epitypes, with variable involvement of transcription factors influencing promoter, enhancer, and repressed regions. Patients in epitypes with stem-cell-like methylation features showed inferior overall survival along with up-regulated stem cell gene expression signatures. We further identified a DNA methylation signature involving STAT motifs associated with FLT3-ITD mutations. Finally, DNA methylation signatures were stable at relapse for the large majority of patients, and rare epitype switching accompanied loss of the dominant epitype mutations and reversion to stem-cell-like methylation patterns. These results show that DNA methylation-based classification integrates important molecular features of AML to reveal the diverse pathogenic and biological aspects of the disease.
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Affiliation(s)
- Brian Giacopelli
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Min Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ada Cleary
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Yue-Zhong Wu
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Anna Reister Schultz
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Maximilian Schmutz
- Hematology and Oncology, Medical Faculty, University of Augsburg, 86159 Augsburg, Germany
| | - James S Blachly
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA.,Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ann-Kathrin Eisfeld
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Bethany Mundy-Bosse
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Sebastian Vosberg
- Department of Medicine III, University Hospital, LMU Munich, 80539 Munich, Germany.,Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Munich, Germany
| | - Philipp A Greif
- Department of Medicine III, University Hospital, LMU Munich, 80539 Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, 69120 Heidelberg, Germany.,German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Rainer Claus
- Department of Medicine II, Stem Cell Transplantation Unit, Klinikum Augsburg, Ludwig-Maximilians University Munich, 86156 Munich, Germany
| | - Lars Bullinger
- Department of Hematology, Oncology and Tumorimmunology, Charité-Universitätsmedizin, 13353 Berlin, Germany
| | - Ramiro Garzon
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Kevin R Coombes
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Clara D Bloomfield
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - John C Byrd
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Christopher C Oakes
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA.,Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA
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42
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Ultimate Precision: Targeting Cancer But Not Normal Self-Replication. Lung Cancer 2021. [DOI: 10.1007/978-3-030-74028-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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43
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Regulating the Regulators: The Role of Histone Deacetylase 1 (HDAC1) in Erythropoiesis. Int J Mol Sci 2020; 21:ijms21228460. [PMID: 33187090 PMCID: PMC7696854 DOI: 10.3390/ijms21228460] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023] Open
Abstract
Histone deacetylases (HDACs) play important roles in transcriptional regulation in eukaryotic cells. Class I deacetylase HDAC1/2 often associates with repressor complexes, such as Sin3 (Switch Independent 3), NuRD (Nucleosome remodeling and deacetylase) and CoREST (Corepressor of RE1 silencing transcription factor) complexes. It has been shown that HDAC1 interacts with and modulates all essential transcription factors for erythropoiesis. During erythropoiesis, histone deacetylase activity is dramatically reduced. Consistently, inhibition of HDAC activity promotes erythroid differentiation. The reduction of HDAC activity not only results in the activation of transcription activators such as GATA-1 (GATA-binding factor 1), TAL1 (TAL BHLH Transcription Factor 1) and KLF1 (Krüpple-like factor 1), but also represses transcription repressors such as PU.1 (Putative oncogene Spi-1). The reduction of histone deacetylase activity is mainly through HDAC1 acetylation that attenuates HDAC1 activity and trans-repress HDAC2 activity through dimerization with HDAC1. Therefore, the acetylation of HDAC1 can convert the corepressor complex to an activator complex for gene activation. HDAC1 also can deacetylate non-histone proteins that play a role on erythropoiesis, therefore adds another layer of gene regulation through HDAC1. Clinically, it has been shown HDACi can reactivate fetal globin in adult erythroid cells. This review will cover the up to date research on the role of HDAC1 in modulating key transcription factors for erythropoiesis and its clinical relevance.
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44
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Wu J, Krchma K, Lee HJ, Prabhakar S, Wang X, Zhao H, Xing X, Seong RH, Fremont DH, Artyomov MN, Wang T, Choi K. Requisite Chromatin Remodeling for Myeloid and Erythroid Lineage Differentiation from Erythromyeloid Progenitors. Cell Rep 2020; 33:108395. [PMID: 33207205 PMCID: PMC7694876 DOI: 10.1016/j.celrep.2020.108395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 09/25/2020] [Accepted: 10/26/2020] [Indexed: 12/21/2022] Open
Abstract
The mammalian SWitch/Sucrose Non-Fermentable (SWI/SNF) chromatin-remodeling BAF (BRG1/BRM-associated factor) complex plays an essential role in developmental and pathological processes. We show that the deletion of Baf155, which encodes a subunit of the BAF complex, in the Tie2(+) lineage (Baf155 (CKO) leads to defects in yolk sac myeloid and definitive erythroid (EryD) lineage differentiation from erythromyeloid progenitors (EMPs). The chromatin of myeloid gene loci in Baf155 CKO EMPs is mostly inaccessible and enriched mainly by the ETS binding motif. BAF155 interacts with PU.1 and is recruited to PU.1 target gene loci together with p300 and KDM6a. Treatment of Baf155 CKO embryos with GSK126, an H3K27me2/3 methyltransferase EZH2 inhibitor, rescues myeloid lineage gene expression. This study uncovers indispensable BAF-mediated chromatin remodeling of myeloid gene loci at the EMP stage. Future studies exploiting epigenetics in the generation and application of EMP derivatives for tissue repair, regeneration, and disease are warranted. The mammalian chromatin-remodeling BAF (BRG1/BRM-associated factor) complex has an essential role in developmental and pathological processes. Wu et al. show that BAF-mediated chromatin remodeling and activation of the myeloid and definitive erythroid transcriptional program at the EMP stage is critical for myeloid and definitive erythroid lineage development.
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Affiliation(s)
- Jun Wu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Karen Krchma
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Hyung Joo Lee
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Sairam Prabhakar
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Xiaoli Wang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Haiyong Zhao
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Xiaoyun Xing
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rho H Seong
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
| | - Daved H Fremont
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA; McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Kyunghee Choi
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA; Graduate School of Biotechnology, Kyung Hee University, Yong In, Korea.
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45
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Srivastava P, Tzetzo SL, Gomez EC, Eng KH, Jani Sait SN, Kuechle JB, Singh PK, De Jong K, Wiatrowski KR, Peresie J, Dimitroff A, Lynch ML, Wang J, Abrams SI, Griffiths EA, Nemeth MJ. Inhibition of LSD1 in MDS progenitors restores differentiation of CD141 Hi conventional dendritic cells. Leukemia 2020; 34:2460-2472. [PMID: 32099035 PMCID: PMC7483249 DOI: 10.1038/s41375-020-0765-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 01/14/2020] [Accepted: 02/12/2020] [Indexed: 11/09/2022]
Abstract
The use of immunotherapy to treat patients with myelodysplastic syndromes (MDS) shows promise but is limited by our incomplete understanding of the immunologic milieu. In solid tumors, CD141Hi conventional dendritic cells (CD141Hi cDCs) are necessary for antitumor immunosurveillance and the response to immunotherapy. Here, we found that CD141Hi cDCs are reduced in MDS bone marrow and based on the premise established in solid tumors, we hypothesized that reduced numbers of CD141Hi cDCs are associated with inferior overall survival in MDS patients. We found that MDS patients with reduced numbers of CD141Hi cDCs, but not other DC populations, showed reduced overall survival. To examine the basis for reduction in CD141Hi cDCs, we found fewer numbers of progenitors committed to DC differentiation in the MDS bone marrow and these progenitors expressed lower levels of interferon regulatory factor-8 (IRF8), a master regulator of CD141Hi cDC differentiation. To rescue impaired CD141Hi cDC differentiation, we used pharmacologic inhibition of lysine-specific demethylase 1A (LSD1) to promote CD141Hi cDC differentiation by MDS progenitors. These data reveal a previously unrecognized element of the MDS immunologic milieu. Epigenetic regulation of CD141Hi cDC differentiation offers an intriguing opportunity for intervention and a potential adjunct to immunotherapy for patients with MDS.
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Affiliation(s)
- Pragya Srivastava
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA
| | - Stephanie L Tzetzo
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA
| | - Eduardo Cortes Gomez
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA
| | - Kevin H Eng
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA
| | - Sheila N Jani Sait
- Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA
| | - Joseph B Kuechle
- Department of Orthopaedics, University at Buffalo, Buffalo, NY, USA
| | - Prashant K Singh
- Center for Personalized Medicine, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA
| | - Kitty De Jong
- Flow and Image Cytometry Shared Resource, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA
| | - Kyle R Wiatrowski
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA
| | - Jennifer Peresie
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA
| | - Ava Dimitroff
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA
| | - Miranda L Lynch
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA
| | - Jianmin Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA
| | - Scott I Abrams
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA
| | - Elizabeth A Griffiths
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA.
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA.
| | - Michael J Nemeth
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA.
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA.
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46
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Su A, Ling F, Vaganay C, Sodaro G, Benaksas C, Dal Bello R, Forget A, Pardieu B, Lin KH, Rutter JC, Bassil CF, Fortin G, Pasanisi J, Antony-Debré I, Alexe G, Benoist JF, Pruvost A, Pikman Y, Qi J, Schlageter MH, Micol JB, Roti G, Cluzeau T, Dombret H, Preudhomme C, Fenouille N, Benajiba L, Golan HM, Stegmaier K, Lobry C, Wood KC, Itzykson R, Puissant A. The Folate Cycle Enzyme MTHFR Is a Critical Regulator of Cell Response to MYC-Targeting Therapies. Cancer Discov 2020; 10:1894-1911. [PMID: 32826232 DOI: 10.1158/2159-8290.cd-19-0970] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 07/02/2020] [Accepted: 08/18/2020] [Indexed: 01/12/2023]
Abstract
Deciphering the impact of metabolic intervention on response to anticancer therapy may elucidate a path toward improved clinical responses. Here, we identify amino acid-related pathways connected to the folate cycle whose activation predicts sensitivity to MYC-targeting therapies in acute myeloid leukemia (AML). We establish that folate restriction and deficiency of the rate-limiting folate cycle enzyme MTHFR, which exhibits reduced-function polymorphisms in about 10% of Caucasians, induce resistance to MYC targeting by BET and CDK7 inhibitors in cell lines, primary patient samples, and syngeneic mouse models of AML. Furthermore, this effect is abrogated by supplementation with the MTHFR enzymatic product CH3-THF. Mechanistically, folate cycle disturbance reduces H3K27/K9 histone methylation and activates a SPI1 transcriptional program counteracting the effect of BET inhibition. Our data provide a rationale for screening MTHFR polymorphisms and folate cycle status to nominate patients most likely to benefit from MYC-targeting therapies. SIGNIFICANCE: Although MYC-targeting therapies represent a promising strategy for cancer treatment, evidence of predictors of sensitivity to these agents is limited. We pinpoint that folate cycle disturbance and frequent polymorphisms associated with reduced MTHFR activity promote resistance to BET inhibitors. CH3-THF supplementation thus represents a low-risk intervention to enhance their effects.See related commentary by Marando and Huntly, p. 1791.This article is highlighted in the In This Issue feature, p. 1775.
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Affiliation(s)
- Angela Su
- INSERM UMR 944, IRSL, St Louis Hospital, University of Paris, Paris, France
| | - Frank Ling
- INSERM UMR 944, IRSL, St Louis Hospital, University of Paris, Paris, France
| | - Camille Vaganay
- INSERM UMR 944, IRSL, St Louis Hospital, University of Paris, Paris, France
| | - Gaetano Sodaro
- INSERM UMR 944, IRSL, St Louis Hospital, University of Paris, Paris, France
| | - Chaïma Benaksas
- INSERM UMR 944, IRSL, St Louis Hospital, University of Paris, Paris, France
| | - Reinaldo Dal Bello
- INSERM UMR 944, IRSL, St Louis Hospital, University of Paris, Paris, France
| | - Antoine Forget
- INSERM UMR 944, IRSL, St Louis Hospital, University of Paris, Paris, France
| | - Bryann Pardieu
- INSERM UMR 944, IRSL, St Louis Hospital, University of Paris, Paris, France
| | - Kevin H Lin
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
| | - Justine C Rutter
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
| | - Christopher F Bassil
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
| | - Gael Fortin
- INSERM UMR 944, IRSL, St Louis Hospital, University of Paris, Paris, France
| | - Justine Pasanisi
- INSERM UMR 944, IRSL, St Louis Hospital, University of Paris, Paris, France
| | - Iléana Antony-Debré
- INSERM UMR 1287, Gustave Roussy Institute, Université Paris-Saclay, Villejuif, France
| | - Gabriela Alexe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.,The Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | | | - Alain Pruvost
- Paris-Saclay University, CEA, INRAE, Département Médicaments et Technologies pour la santé, SPI, Gif-sur-Yvette, France
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Cancer Biology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jun Qi
- The Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, Massachusetts.,Department of Cancer Biology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Marie-Hélène Schlageter
- AP-HP, Cellular Biology Department, St Louis Hospital, Paris, France.,INSERM U 1131, IRSL, St Louis Hospital, University of Paris, Paris, France
| | - Jean-Baptiste Micol
- INSERM UMR 1287, Gustave Roussy Institute, Université Paris-Saclay, Villejuif, France.,Department of Hematology, Gustave Roussy Institute, Villejuif, France
| | - Giovanni Roti
- University of Parma, Department of Medicine and Surgery, Parma, Italy
| | - Thomas Cluzeau
- Department of Hematology, Centre Hospitalier Universitaire, Nice, France
| | | | | | - Nina Fenouille
- INSERM UMR 944, IRSL, St Louis Hospital, University of Paris, Paris, France
| | - Lina Benajiba
- INSERM UMR 944, IRSL, St Louis Hospital, University of Paris, Paris, France.,AP-HP, Hematology Department, St Louis Hospital, Paris, France
| | - Hava M Golan
- Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.,The Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Camille Lobry
- INSERM UMR 1287, Gustave Roussy Institute, Université Paris-Saclay, Villejuif, France
| | - Kris C Wood
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
| | - Raphael Itzykson
- INSERM UMR 944, IRSL, St Louis Hospital, University of Paris, Paris, France.
| | - Alexandre Puissant
- INSERM UMR 944, IRSL, St Louis Hospital, University of Paris, Paris, France.
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47
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McKenzie MD, Ghisi M, Oxley EP, Ngo S, Cimmino L, Esnault C, Liu R, Salmon JM, Bell CC, Ahmed N, Erlichster M, Witkowski MT, Liu GJ, Chopin M, Dakic A, Simankowicz E, Pomilio G, Vu T, Krsmanovic P, Su S, Tian L, Baldwin TM, Zalcenstein DA, DiRago L, Wang S, Metcalf D, Johnstone RW, Croker BA, Lancaster GI, Murphy AJ, Naik SH, Nutt SL, Pospisil V, Schroeder T, Wall M, Dawson MA, Wei AH, de Thé H, Ritchie ME, Zuber J, Dickins RA. Interconversion between Tumorigenic and Differentiated States in Acute Myeloid Leukemia. Cell Stem Cell 2020; 25:258-272.e9. [PMID: 31374198 DOI: 10.1016/j.stem.2019.07.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 01/28/2019] [Accepted: 07/01/2019] [Indexed: 12/11/2022]
Abstract
Tumors are composed of phenotypically heterogeneous cancer cells that often resemble various differentiation states of their lineage of origin. Within this hierarchy, it is thought that an immature subpopulation of tumor-propagating cancer stem cells (CSCs) differentiates into non-tumorigenic progeny, providing a rationale for therapeutic strategies that specifically eradicate CSCs or induce their differentiation. The clinical success of these approaches depends on CSC differentiation being unidirectional rather than reversible, yet this question remains unresolved even in prototypically hierarchical malignancies, such as acute myeloid leukemia (AML). Here, we show in murine and human models of AML that, upon perturbation of endogenous expression of the lineage-determining transcription factor PU.1 or withdrawal of established differentiation therapies, some mature leukemia cells can de-differentiate and reacquire clonogenic and leukemogenic properties. Our results reveal plasticity of CSC maturation in AML, highlighting the need to therapeutically eradicate cancer cells across a range of differentiation states.
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Affiliation(s)
- Mark D McKenzie
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Margherita Ghisi
- Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia
| | - Ethan P Oxley
- Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia
| | - Steven Ngo
- Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia
| | - Luisa Cimmino
- Department of Pathology, New York University School of Medicine, 550 1(st) Avenue, New York, NY 10016, USA
| | - Cécile Esnault
- Collège de France, PSL Research University, 75005 Paris, France; INSERM U944, CNRS UMR7212, Université de Paris, Institut de Recherche Saint Louis, 75010 Paris, France; Assistance Publique/Hôpitaux de Paris, Oncologie Moléculaire, Hôpital St. Louis, 75010 Paris, France
| | - Ruijie Liu
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Jessica M Salmon
- Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia
| | - Charles C Bell
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Nouraiz Ahmed
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Michael Erlichster
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Matthew T Witkowski
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia; Department of Pathology, New York University School of Medicine, 550 1(st) Avenue, New York, NY 10016, USA; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Grace J Liu
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Michael Chopin
- Molecular Immunology Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Aleksandar Dakic
- Molecular Immunology Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Emilia Simankowicz
- Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia
| | - Giovanna Pomilio
- Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia; Department of Clinical Haematology, The Alfred Hospital, Melbourne, VIC 3004, Australia
| | - Tina Vu
- Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia
| | - Pavle Krsmanovic
- Institute of Pathological Physiology and Biocev, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Shian Su
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Luyi Tian
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Tracey M Baldwin
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Daniela A Zalcenstein
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Ladina DiRago
- Cancer and Haematology Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Shu Wang
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Donald Metcalf
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia; Cancer and Haematology Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Ricky W Johnstone
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Ben A Croker
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Graeme I Lancaster
- Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; Department of Immunology and Pathology, Monash University, Commercial Road, Melbourne, VIC 3004, Australia
| | - Andrew J Murphy
- Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; Department of Immunology and Pathology, Monash University, Commercial Road, Melbourne, VIC 3004, Australia
| | - Shalin H Naik
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Stephen L Nutt
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia; Molecular Immunology Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Vitek Pospisil
- Institute of Pathological Physiology and Biocev, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Timm Schroeder
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Meaghan Wall
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia; Victorian Cancer Cytogenetics Service, St. Vincent's Hospital, 41 Victoria Parade, Fitzroy, VIC 3065, Australia
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Andrew H Wei
- Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia; Department of Clinical Haematology, The Alfred Hospital, Melbourne, VIC 3004, Australia
| | - Hugues de Thé
- Collège de France, PSL Research University, 75005 Paris, France; INSERM U944, CNRS UMR7212, Université de Paris, Institut de Recherche Saint Louis, 75010 Paris, France; Assistance Publique/Hôpitaux de Paris, Oncologie Moléculaire, Hôpital St. Louis, 75010 Paris, France
| | - Matthew E Ritchie
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia; School of Mathematics and Statistics, University of Melbourne, Parkville, VIC 3010, Australia
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Campus Vienna Biocenter 1, 1030 Vienna, Austria; Medical University of Vienna, 1030 Vienna, Austria
| | - Ross A Dickins
- Australian Centre for Blood Diseases, Monash University, Commercial Road, Melbourne, VIC 3004, Australia.
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Blood disease-causing and -suppressing transcriptional enhancers: general principles and GATA2 mechanisms. Blood Adv 2020; 3:2045-2056. [PMID: 31289032 DOI: 10.1182/bloodadvances.2019000378] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 05/29/2019] [Indexed: 12/16/2022] Open
Abstract
Intensive scrutiny of human genomes has unveiled considerable genetic variation in coding and noncoding regions. In cancers, including those of the hematopoietic system, genomic instability amplifies the complexity and functional consequences of variation. Although elucidating how variation impacts the protein-coding sequence is highly tractable, deciphering the functional consequences of variation in noncoding regions (genome reading), including potential transcriptional-regulatory sequences, remains challenging. A crux of this problem is the sheer abundance of gene-regulatory sequence motifs (cis elements) mediating protein-DNA interactions that are intermixed in the genome with thousands of look-alike sequences lacking the capacity to mediate functional interactions with proteins in vivo. Furthermore, transcriptional enhancers harbor clustered cis elements, and how altering a single cis element within a cluster impacts enhancer function is unpredictable. Strategies to discover functional enhancers have been innovated, and human genetics can provide vital clues to achieve this goal. Germline or acquired mutations in functionally critical (essential) enhancers, for example at the GATA2 locus encoding a master regulator of hematopoiesis, have been linked to human pathologies. Given the human interindividual genetic variation and complex genetic landscapes of hematologic malignancies, enhancer corruption, creation, and expropriation by new genes may not be exceedingly rare mechanisms underlying disease predisposition and etiology. Paradigms arising from dissecting essential enhancer mechanisms can guide genome-reading strategies to advance fundamental knowledge and precision medicine applications. In this review, we provide our perspective of general principles governing the function of blood disease-linked enhancers and GATA2-centric mechanisms.
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Shin E, Jeong JG, Chung H, Jung H, Park C, Yoon SR, Kim TD, Lee SJ, Choi I, Noh JY. The Gata1 murine megakaryocyte–erythroid progenitor cells expand robustly and alter differentiation potential. Biochem Biophys Res Commun 2020; 528:46-53. [DOI: 10.1016/j.bbrc.2020.04.143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/26/2020] [Accepted: 04/29/2020] [Indexed: 12/20/2022]
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50
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Wheat JC, Sella Y, Willcockson M, Skoultchi AI, Bergman A, Singer RH, Steidl U. Single-molecule imaging of transcription dynamics in somatic stem cells. Nature 2020; 583:431-436. [PMID: 32581360 PMCID: PMC8577313 DOI: 10.1038/s41586-020-2432-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 03/31/2020] [Indexed: 12/17/2022]
Abstract
Molecular noise is a natural phenomenon inherent to all biological systems1,2. How stochastic processes give rise to the robust outcomes supportive of tissue homeostasis is a conundrum. Here, to quantitatively investigate this issue, we use single-molecule mRNA FISH (smFISH) on stem cells derived from hematopoietic tissue to measure the transcription dynamics of three key transcription factor (TF) genes: PU.1, Gata1 and Gata2. Our results indicate that infrequent, stochastic bursts of transcription result in the co-expression of these antagonistic TF in the majority of hematopoietic stem and progenitor cells. Moreover, by pairing smFISH to time-lapse microscopy and the analysis of pedigrees, we find that while individual stem cell clones produce offspring that are in transcriptionally related states, akin to a transcriptional priming phenomenon, the underlying transition dynamics between states are nevertheless best captured by stochastic and reversible models. As such, the outcome of a stochastic process can produce cellular behaviors that may be incorrectly inferred to have arisen from deterministic dynamics. In light of our findings, we propose a model whereby the intrinsic stochasticity of gene expression facilitates, rather than impedes, concomitant maintenance of transcriptional plasticity and stem cell robustness.
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Affiliation(s)
- Justin C Wheat
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA.,Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, New York, NY, USA
| | - Yehonatan Sella
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Michael Willcockson
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Arthur I Skoultchi
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Aviv Bergman
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, New York, NY, USA.,Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, NY, USA.,Department of Pathology, Albert Einstein College of Medicine, New York, NY, USA.,Santa Fe Institute, Santa Fe, NM, USA
| | - Robert H Singer
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA.,Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, NY, USA.,Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY, USA.,Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, New York, NY, USA.,Janelia Research Campus of the HHMI, Ashburn, VA, USA
| | - Ulrich Steidl
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA. .,Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, New York, NY, USA. .,Department of Medicine (Oncology), Albert Einstein College of Medicine-Montefiore Medical Center, New York, NY, USA. .,Albert Einstein Cancer Center, Albert Einstein College of Medicine, New York, NY, USA.
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