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Ando K, Ou J, Thompson JD, Welsby J, Bangru S, Shen J, Wei X, Diao Y, Poss KD. A screen for regeneration-associated silencer regulatory elements in zebrafish. Dev Cell 2024; 59:676-691.e5. [PMID: 38290519 PMCID: PMC10939760 DOI: 10.1016/j.devcel.2024.01.004] [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: 06/24/2023] [Revised: 11/03/2023] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
Regeneration involves gene expression changes explained in part by context-dependent recruitment of transcriptional activators to distal enhancers. Silencers that engage repressive transcriptional complexes are less studied than enhancers and more technically challenging to validate, but they potentially have profound biological importance for regeneration. Here, we identified candidate silencers through a screening process that examined the ability of DNA sequences to limit injury-induced gene expression in larval zebrafish after fin amputation. A short sequence (s1) on chromosome 5 near several genes that reduce expression during adult fin regeneration could suppress promoter activity in stable transgenic lines and diminish nearby gene expression in knockin lines. High-resolution analysis of chromatin organization identified physical associations of s1 with gene promoters occurring preferentially during fin regeneration, and genomic deletion of s1 elevated the expression of these genes after fin amputation. Our study provides methods to identify "tissue regeneration silencer elements" (TRSEs) with the potential to reduce unnecessary or deleterious gene expression during regeneration.
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Affiliation(s)
- Kazunori Ando
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jianhong Ou
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - John D Thompson
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - John Welsby
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sushant Bangru
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jingwen Shen
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaolin Wei
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yarui Diao
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kenneth D Poss
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA.
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2
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Katsumura KR, Liu P, Kim JA, Mehta C, Bresnick EH. Pathogenic GATA2 genetic variants utilize an obligate enhancer mechanism to distort a multilineage differentiation program. Proc Natl Acad Sci U S A 2024; 121:e2317147121. [PMID: 38422019 DOI: 10.1073/pnas.2317147121] [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: 10/06/2023] [Accepted: 01/04/2024] [Indexed: 03/02/2024] Open
Abstract
Mutations in genes encoding transcription factors inactivate or generate ectopic activities to instigate pathogenesis. By disrupting hematopoietic stem/progenitor cells, GATA2 germline variants create a bone marrow failure and leukemia predisposition, GATA2 deficiency syndrome, yet mechanisms underlying the complex phenotypic constellation are unresolved. We used a GATA2-deficient progenitor rescue system to analyze how genetic variation influences GATA2 functions. Pathogenic variants impaired, without abrogating, GATA2-dependent transcriptional regulation. Variants promoted eosinophil and repressed monocytic differentiation without regulating mast cell and erythroid differentiation. While GATA2 and T354M required the DNA-binding C-terminal zinc finger, T354M disproportionately required the N-terminal finger and N terminus. GATA2 and T354M activated a CCAAT/Enhancer Binding Protein-ε (C/EBPε) enhancer, creating a feedforward loop operating with the T-cell Acute Lymphocyte Leukemia-1 (TAL1) transcription factor. Elevating C/EBPε partially normalized hematopoietic defects of GATA2-deficient progenitors. Thus, pathogenic germline variation discriminatively spares or compromises transcription factor attributes, and retaining an obligate enhancer mechanism distorts a multilineage differentiation program.
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Affiliation(s)
- Koichi R Katsumura
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705
| | - Peng Liu
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705
- Cancer Informatics Shared Resource, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705
| | - Jeong-Ah Kim
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705
| | - Charu Mehta
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705
| | - Emery H Bresnick
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705
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3
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Wang Y, Chen KP. C and G are frequently mutated into T and A in coding regions of human genes. Mol Genet Genomics 2024; 299:23. [PMID: 38431687 DOI: 10.1007/s00438-024-02118-5] [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: 10/05/2023] [Accepted: 01/24/2024] [Indexed: 03/05/2024]
Abstract
Nucleotide mutations in human genes have long been a hot subject for study because some of them may lead to severe human diseases. Understanding the general mutational process and evolutionary trend of human genes could help answer such questions as why certain diseases occur and what challenges we face in protecting human health. In this study, we conducted statistics on 89,895 single-nucleotide variations identified in coding regions of 18,339 human genes. The results show that C and G are frequently mutated into T and A in human genes. C/G (C or G)-to-T/A mutations lead to reduction of hydrogen bonds in double-stranded DNA because C-G and T-A base pairs are maintained by three and two hydrogen bonds respectively. C-to-T and G-to-A mutations occur predominantly in human genes because they not only reduce hydrogen bonds but also belong to transition mutation. Reduction of hydrogen bonds could reduce energy consumption not only in separating double strands of mutated DNA for transcription and replication but also in disrupting stem-loop structure of mutated mRNA for translation. It is thus considered that to reduce hydrogen bonds (and thus to reduce energy consumption in gene expression) is one of the driving forces for nucleotide mutation. Moreover, codon mutation is positively correlated to its content, suggesting that most mutations are not targeted on changing any specific codons (amino acids) but are merely for reducing hydrogen bonds. Our study provides an example of utilizing single-nucleotide variation data to infer evolutionary trend of human genes, which can be referenced to conduct similar studies in other organisms.
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Affiliation(s)
- Yong Wang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China.
| | - Ke-Ping Chen
- School of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China
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4
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Lin F, Cao K, Chang F, Oved JH, Luo M, Fan Z, Schubert J, Wu J, Zhong Y, Gallo DJ, Denenberg EH, Chen J, Fanning EA, Lambert MP, Paessler ME, Surrey LF, Zelley K, MacFarland S, Kurre P, Olson TS, Li MM. Uncovering the Genetic Etiology of Inherited Bone Marrow Failure Syndromes Using a Custom-Designed Next-Generation Sequencing Panel. J Mol Diagn 2024; 26:191-201. [PMID: 38103590 DOI: 10.1016/j.jmoldx.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 09/13/2023] [Accepted: 11/20/2023] [Indexed: 12/19/2023] Open
Abstract
Inherited bone marrow failure syndromes (IBMFS) are a group of heterogeneous disorders that account for ∼30% of pediatric cases of bone marrow failure and are often associated with developmental abnormalities and cancer predisposition. This article reports the laboratory validation and clinical utility of a large-scale, custom-designed next-generation sequencing panel, Children's Hospital of Philadelphia (CHOP) IBMFS panel, for the diagnosis of IBMFS in a cohort of pediatric patients. This panel demonstrated excellent analytic accuracy, with 100% sensitivity, ≥99.99% specificity, and 100% reproducibility on validation samples. In 269 patients with suspected IBMFS, this next-generation sequencing panel was used for identifying single-nucleotide variants, small insertions/deletions, and copy number variations in mosaic or nonmosaic status. Sixty-one pathogenic/likely pathogenic variants (54 single-nucleotide variants/insertions/deletions and 7 copy number variations) and 24 hypomorphic variants were identified, resulting in the molecular diagnosis of IBMFS in 21 cases (7.8%) and exclusion of IBMFS with a diagnosis of a blood disorder in 10 cases (3.7%). Secondary findings, including evidence of early hematologic malignancies and other hereditary cancer-predisposition syndromes, were observed in 9 cases (3.3%). The CHOP IBMFS panel was highly sensitive and specific, with a significant increase in the diagnostic yield of IBMFS. These findings suggest that next-generation sequencing-based panel testing should be a part of routine diagnostics in patients with suspected IBMFS.
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Affiliation(s)
- Fumin Lin
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Kajia Cao
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Fengqi Chang
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Joseph H Oved
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Minjie Luo
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Zhiqian Fan
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jeffrey Schubert
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jinhua Wu
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Yiming Zhong
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Daniel J Gallo
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Elizabeth H Denenberg
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jiani Chen
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Elizabeth A Fanning
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Michele P Lambert
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Pediatric Comprehensive Bone Marrow Failure Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Michele E Paessler
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Lea F Surrey
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kristin Zelley
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Suzanne MacFarland
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Peter Kurre
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Pediatric Comprehensive Bone Marrow Failure Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Timothy S Olson
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Pediatric Comprehensive Bone Marrow Failure Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Marilyn M Li
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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5
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Soukup AA, Bresnick EH. Gata2 noncoding genetic variation as a determinant of hematopoietic stem/progenitor cell mobilization efficiency. Blood Adv 2023; 7:7564-7575. [PMID: 37871305 PMCID: PMC10761364 DOI: 10.1182/bloodadvances.2023011003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/25/2023] Open
Abstract
Germline genetic variants alter the coding and enhancer sequences of GATA2, which encodes a master regulator of hematopoiesis. The conserved murine Gata2 enhancer (+9.5) promotes hematopoietic stem cell (HSC) genesis during embryogenesis. Heterozygosity for a single-nucleotide Ets motif variant in the human enhancer creates a bone marrow failure and acute myeloid leukemia predisposition termed GATA2 deficiency syndrome. The homozygous murine variant attenuates chemotherapy- and transplantation-induced hematopoietic regeneration, hematopoietic stem and progenitor cell (HSPC) response to inflammation, and HSPC mobilization with the therapeutic mobilizer granulocyte colony-stimulating factor (G-CSF). Because a Gata2 +9.5 variant attenuated G-CSF-induced HSPC expansion and mobilization, and HSC transplantation therapies require efficacious mobilization, we tested whether variation affects mechanistically distinct mobilizers or only those operating through select pathways. In addition to affecting G-CSF activity, Gata2 variation compromised IL-8/CXCR2- and VLA-4/VCAM1-induced mobilization. Although the variation did not disrupt HSPC mobilization mediated by plerixafor, which functions through CXCR4/CXCL12, homozygous and heterozygous variation attenuated mobilization efficacy of the clinically used plerixafor/G-CSF combination. The influence of noncoding variation on HSPC mobilization efficacy and function is important clinically because comprehensive noncoding variation is not commonly analyzed in patients. Furthermore, our mobilization-defective system offers unique utility for elucidating fundamental HSPC mechanisms.
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Affiliation(s)
- Alexandra A. Soukup
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Emery H. Bresnick
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI
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6
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Zhou Y, Dogiparthi VR, Ray S, Schaefer MA, Harris HL, Rowley MJ, Hewitt KJ. Defining a cohort of anemia-activated cis elements reveals a mechanism promoting erythroid precursor function. Blood Adv 2023; 7:6325-6338. [PMID: 36809789 PMCID: PMC10587717 DOI: 10.1182/bloodadvances.2022009163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/09/2023] [Accepted: 01/24/2023] [Indexed: 02/24/2023] Open
Abstract
Acute anemia elicits broad transcriptional changes in erythroid progenitors and precursors. We previously discovered a cis-regulatory transcriptional enhancer at the sterile alpha motif domain-14 enhancer locus (S14E), defined by a CANNTG-spacer-AGATAA composite motif and occupied by GATA1 and TAL1 transcription factors, is required for survival in severe anemia. However, S14E is only 1 of dozens of anemia-activated genes containing similar motifs. In a mouse model of acute anemia, we identified populations of expanding erythroid precursors, which increased expression of genes that contain S14E-like cis elements. We reveal that several S14E-like cis elements provide important transcriptional control of newly identified anemia-inducing genes, including the Ssx-2 interacting protein (Ssx2ip). Ssx2ip expression was determined to play an important role in erythroid progenitor/precursor cell activities, cell cycle regulation, and cell proliferation. Over a weeklong course of acute anemia recovery, we observed that erythroid gene activation mediated by S14E-like cis elements occurs during a phase coincident with low hematocrit and high progenitor activities, with distinct transcriptional programs activated at earlier and later time points. Our results define a genome-wide mechanism in which S14E-like enhancers control transcriptional responses during erythroid regeneration. These findings provide a framework to understand anemia-specific transcriptional mechanisms, ineffective erythropoiesis, anemia recovery, and phenotypic variability within human populations.
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Affiliation(s)
- Yichao Zhou
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE
| | | | - Suhita Ray
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE
| | - Meg A. Schaefer
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE
| | - Hannah L. Harris
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE
| | - M. Jordan Rowley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE
| | - Kyle J. Hewitt
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE
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7
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West RR, Bauer TR, Tuschong LM, Embree LJ, Calvo KR, Tillo D, Davis J, Holland SM, Hickstein DD. A novel GATA2 distal enhancer mutation results in MonoMAC syndrome in 2 second cousins. Blood Adv 2023; 7:6351-6363. [PMID: 37595058 PMCID: PMC10587712 DOI: 10.1182/bloodadvances.2023010458] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/24/2023] [Accepted: 08/12/2023] [Indexed: 08/20/2023] Open
Abstract
Mutations in the transcription factor GATA2 can cause MonoMAC syndrome, a GATA2 deficiency disease characterized by several findings, including disseminated nontuberculous mycobacterial infections, severe deficiencies of monocytes, natural killer cells, and B lymphocytes, and myelodysplastic syndrome. GATA2 mutations are found in ∼90% of patients with a GATA2 deficiency phenotype and are largely missense mutations in the conserved second zinc-finger domain. Mutations in an intron 5 regulatory enhancer element are also well described in GATA2 deficiency. Here, we present a multigeneration kindred with the clinical features of GATA2 deficiency but lacking an apparent GATA2 mutation. Whole genome sequencing revealed a unique adenine-to-thymine variant in the GATA2 -110 enhancer 116,855 bp upstream of the GATA2 ATG start site. The mutation creates a new E-box consensus in position with an existing GATA-box to generate a new hematopoietic regulatory composite element. The mutation segregates with the disease in several generations of the family. Cell type-specific allelic imbalance of GATA2 expression was observed in the bone marrow of a patient with higher expression from the mutant-linked allele. Allele-specific overexpression of GATA2 was observed in CRISPR/Cas9-modified HL-60 cells and in luciferase assays with the enhancer mutation. This study demonstrates overexpression of GATA2 resulting from a single nucleotide change in an upstream enhancer element in patients with MonoMAC syndrome. Patients in this study were enrolled in the National Institute of Allergy and Infectious Diseases clinical trial and the National Cancer Institute clinical trial (both trials were registered at www.clinicaltrials.gov as #NCT01905826 and #NCT01861106, respectively).
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Affiliation(s)
- Robert R. West
- Immune Deficiency–Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Thomas R. Bauer
- Immune Deficiency–Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Laura M. Tuschong
- Immune Deficiency–Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Lisa J. Embree
- Immune Deficiency–Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Katherine R. Calvo
- Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, MD
| | - Desiree Tillo
- Genomics Core, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Joie Davis
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Steven M. Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Dennis D. Hickstein
- Immune Deficiency–Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
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8
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Zoller J, Trajanova D, Feurstein S. Germline and somatic drivers in inherited hematologic malignancies. Front Oncol 2023; 13:1205855. [PMID: 37904876 PMCID: PMC10613526 DOI: 10.3389/fonc.2023.1205855] [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: 04/14/2023] [Accepted: 09/15/2023] [Indexed: 11/01/2023] Open
Abstract
Inherited hematologic malignancies are linked to a heterogenous group of genes, knowledge of which is rapidly expanding using panel-based next-generation sequencing (NGS) or whole-exome/whole-genome sequencing. Importantly, the penetrance for these syndromes is incomplete, and disease development, progression or transformation has critical clinical implications. With the earlier detection of healthy carriers and sequential monitoring of these patients, clonal hematopoiesis and somatic driver variants become significant factors in determining disease transformation/progression and timing of (preemptive) hematopoietic stem cell transplant in these patients. In this review, we shed light on the detection of probable germline predisposition alleles based on diagnostic/prognostic 'somatic' NGS panels. A multi-tier approach including variant allele frequency, bi-allelic inactivation, persistence of a variant upon clinical remission and mutational burden can indicate variants with high pre-test probability. We also discuss the shared underlying biology and frequency of germline and somatic variants affecting the same gene, specifically focusing on variants in DDX41, ETV6, GATA2 and RUNX1. Germline variants in these genes are associated with a (specific) pattern or over-/underrepresentation of somatic molecular or cytogenetic alterations that may help identify the underlying germline syndrome and predict the course of disease in these individuals. This review is based on the current knowledge about somatic drivers in these four syndromes by integrating data from all published patients, thereby providing clinicians with valuable and concise information.
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Affiliation(s)
| | | | - Simone Feurstein
- Department of Internal Medicine, Section of Hematology, Oncology & Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
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9
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Aktar A, Heit B. Role of the pioneer transcription factor GATA2 in health and disease. J Mol Med (Berl) 2023; 101:1191-1208. [PMID: 37624387 DOI: 10.1007/s00109-023-02359-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 08/04/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023]
Abstract
The transcription factor GATA2 is involved in human diseases ranging from hematopoietic disorders, to cancer, to infectious diseases. GATA2 is one of six GATA-family transcription factors that act as pioneering transcription factors which facilitate the opening of heterochromatin and the subsequent binding of other transcription factors to induce gene expression from previously inaccessible regions of the genome. Although GATA2 is essential for hematopoiesis and lymphangiogenesis, it is also expressed in other tissues such as the lung, prostate gland, gastrointestinal tract, central nervous system, placenta, fetal liver, and fetal heart. Gene or transcriptional abnormalities of GATA2 causes or predisposes patients to several diseases including the hematological cancers acute myeloid leukemia and acute lymphoblastic leukemia, the primary immunodeficiency MonoMAC syndrome, and to cancers of the lung, prostate, uterus, kidney, breast, gastric tract, and ovaries. Recent data has also linked GATA2 expression and mutations to responses to infectious diseases including SARS-CoV-2 and Pneumocystis carinii pneumonia, and to inflammatory disorders such as atherosclerosis. In this article we review the role of GATA2 in the etiology and progression of these various diseases.
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Affiliation(s)
- Amena Aktar
- Department of Microbiology and Immunology; the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, ON, N6A 5C1, Canada
| | - Bryan Heit
- Department of Microbiology and Immunology; the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, ON, N6A 5C1, Canada.
- Robarts Research Institute, London, ON, N6A 3K7, Canada.
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10
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Wormser O, Perez Y, Dolgin V, Kamali B, Tangeman JA, Gradstein L, Yogev Y, Hadar N, Freund O, Drabkin M, Halperin D, Irron I, Grajales-Esquivel E, Del Rio-Tsonis K, Birnbaum RY, Akler G, Birk OS. IHH enhancer variant within neighboring NHEJ1 intron causes microphthalmia anophthalmia and coloboma. NPJ Genom Med 2023; 8:22. [PMID: 37580330 PMCID: PMC10425348 DOI: 10.1038/s41525-023-00364-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 07/27/2023] [Indexed: 08/16/2023] Open
Abstract
Genomic sequences residing within introns of few genes have been shown to act as enhancers affecting expression of neighboring genes. We studied an autosomal recessive phenotypic continuum of microphthalmia, anophthalmia and ocular coloboma, with no apparent coding-region disease-causing mutation. Homozygosity mapping of several affected Jewish Iranian families, combined with whole genome sequence analysis, identified a 0.5 Mb disease-associated chromosome 2q35 locus (maximal LOD score 6.8) harboring an intronic founder variant in NHEJ1, not predicted to affect NHEJ1. The human NHEJ1 intronic variant lies within a known specifically limb-development enhancer of a neighboring gene, Indian hedgehog (Ihh), known to be involved in eye development in mice and chickens. Through mouse and chicken molecular development studies, we demonstrated that this variant is within an Ihh enhancer that drives gene expression in the developing eye and that the identified variant affects this eye-specific enhancer activity. We thus delineate an Ihh enhancer active in mammalian eye development whose variant causes human microphthalmia, anophthalmia and ocular coloboma. The findings highlight disease causation by an intronic variant affecting the expression of a neighboring gene, delineating molecular pathways of eye development.
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Affiliation(s)
- Ohad Wormser
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yonatan Perez
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Vadim Dolgin
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Bahman Kamali
- Medical Advisory Committee, United Mashhadi Jewish Community of America, 54 Steamboat Rd., Great Neck, NY, 11024, USA
| | - Jared A Tangeman
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH, 45056, USA
| | - Libe Gradstein
- Department of Ophthalmology, Soroka Medical Center and Clalit Health Services, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yuval Yogev
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Noam Hadar
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ofek Freund
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Max Drabkin
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Daniel Halperin
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Inbar Irron
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Erika Grajales-Esquivel
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH, 45056, USA
| | - Katia Del Rio-Tsonis
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH, 45056, USA
| | - Ramon Y Birnbaum
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Gidon Akler
- TOVANA Health, Houston, TX, USA.
- Precision Medicine Insights, P.C., Great Neck, NY, USA.
| | - Ohad S Birk
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
- Genetics Institute, Soroka Medical Center affiliated to Ben-Gurion University of the Negev, Beer-Sheva, Israel.
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11
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Illi B, Nasi S. Myc beyond Cancer: Regulation of Mammalian Tissue Regeneration. PATHOPHYSIOLOGY 2023; 30:346-365. [PMID: 37606389 PMCID: PMC10443299 DOI: 10.3390/pathophysiology30030027] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/23/2023] Open
Abstract
Myc is one of the most well-known oncogenes driving tumorigenesis in a wide variety of tissues. From the brain to blood, its deregulation derails physiological pathways that grant the correct functioning of the cell. Its action is carried out at the gene expression level, where Myc governs basically every aspect of transcription. Indeed, in addition to its role as a canonical, chromatin-bound transcription factor, Myc rules RNA polymerase II (RNAPII) transcriptional pause-release, elongation and termination and mRNA capping. For this reason, it is evident that minimal perturbations of Myc function mirror malignant cell behavior and, consistently, a large body of literature mainly focuses on Myc malfunctioning. In healthy cells, Myc controls molecular mechanisms involved in pivotal functions, such as cell cycle (and proliferation thereof), apoptosis, metabolism and cell size, angiogenesis, differentiation and stem cell self-renewal. In this latter regard, Myc has been found to also regulate tissue regeneration, a hot topic in the research fields of aging and regenerative medicine. Indeed, Myc appears to have a role in wound healing, in peripheral nerves and in liver, pancreas and even heart recovery. Herein, we discuss the state of the art of Myc's role in tissue regeneration, giving an overview of its potent action beyond cancer.
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Affiliation(s)
- Barbara Illi
- Institute of Molecular Biology and Pathology, National Research Council, c/o Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy
| | - Sergio Nasi
- Institute of Molecular Biology and Pathology, National Research Council, c/o Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy
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12
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Johnson KD, Jung MM, Tran VL, Bresnick EH. Interferon regulatory factor-8-dependent innate immune alarm senses GATA2 deficiency to alter hematopoietic differentiation and function. Curr Opin Hematol 2023; 30:117-123. [PMID: 37254854 PMCID: PMC10236032 DOI: 10.1097/moh.0000000000000763] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
PURPOSE OF REVIEW Recent discoveries have provided evidence for mechanistic links between the master regulator of hematopoiesis GATA2 and the key component of interferon and innate immunity signaling pathways, interferon-regulatory factor-8 (IRF8). These links have important implications for the control of myeloid differentiation in physiological and pathological states. RECENT FINDINGS GATA2 deficiency resulting from loss of the Gata2 -77 enhancer in progenitors triggers an alarm that instigates the transcriptional induction of innate immune signaling and distorts a myeloid differentiation program. This pathological alteration renders progenitors hyperresponsive to interferon γ, toll-like receptor and interleukin-6 signaling and impaired in granulocyte-macrophage colony-stimulating factor signaling. IRF8 upregulation in -77-/- progenitors promotes monocyte and dendritic cell differentiation while suppressing granulocytic differentiation. As PU.1 promotes transcription of Irf8 and other myeloid and B-lineage genes, GATA2-mediated repression of these genes opposes the PU.1-dependent activating mechanism. SUMMARY As GATA2 deficiency syndrome is an immunodeficiency disorder often involving myelodysplastic syndromes and acute myeloid leukemia, elucidating how GATA2 commissions and decommissions genome activity and developmental regulatory programs will unveil mechanisms that go awry when GATA2 levels and/or activities are disrupted.
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Affiliation(s)
- Kirby D Johnson
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
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13
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Tenney AP, Di Gioia SA, Webb BD, Chan WM, de Boer E, Garnai SJ, Barry BJ, Ray T, Kosicki M, Robson CD, Zhang Z, Collins TE, Gelber A, Pratt BM, Fujiwara Y, Varshney A, Lek M, Warburton PE, Van Ryzin C, Lehky TJ, Zalewski C, King KA, Brewer CC, Thurm A, Snow J, Facio FM, Narisu N, Bonnycastle LL, Swift A, Chines PS, Bell JL, Mohan S, Whitman MC, Staffieri SE, Elder JE, Demer JL, Torres A, Rachid E, Al-Haddad C, Boustany RM, Mackey DA, Brady AF, Fenollar-Cortés M, Fradin M, Kleefstra T, Padberg GW, Raskin S, Sato MT, Orkin SH, Parker SCJ, Hadlock TA, Vissers LELM, van Bokhoven H, Jabs EW, Collins FS, Pennacchio LA, Manoli I, Engle EC. Noncoding variants alter GATA2 expression in rhombomere 4 motor neurons and cause dominant hereditary congenital facial paresis. Nat Genet 2023; 55:1149-1163. [PMID: 37386251 PMCID: PMC10335940 DOI: 10.1038/s41588-023-01424-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/10/2023] [Indexed: 07/01/2023]
Abstract
Hereditary congenital facial paresis type 1 (HCFP1) is an autosomal dominant disorder of absent or limited facial movement that maps to chromosome 3q21-q22 and is hypothesized to result from facial branchial motor neuron (FBMN) maldevelopment. In the present study, we report that HCFP1 results from heterozygous duplications within a neuron-specific GATA2 regulatory region that includes two enhancers and one silencer, and from noncoding single-nucleotide variants (SNVs) within the silencer. Some SNVs impair binding of NR2F1 to the silencer in vitro and in vivo and attenuate in vivo enhancer reporter expression in FBMNs. Gata2 and its effector Gata3 are essential for inner-ear efferent neuron (IEE) but not FBMN development. A humanized HCFP1 mouse model extends Gata2 expression, favors the formation of IEEs over FBMNs and is rescued by conditional loss of Gata3. These findings highlight the importance of temporal gene regulation in development and of noncoding variation in rare mendelian disease.
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Affiliation(s)
- Alan P Tenney
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
| | - Silvio Alessandro Di Gioia
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Bryn D Webb
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Wai-Man Chan
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Elke de Boer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Sarah J Garnai
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Harvard-MIT Health Sciences and Technology, Harvard Medical School, Boston, MA, USA
| | - Brenda J Barry
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Tammy Ray
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael Kosicki
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Caroline D Robson
- Department of Radiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zhongyang Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas E Collins
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Alon Gelber
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brandon M Pratt
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yuko Fujiwara
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Arushi Varshney
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Monkol Lek
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Peter E Warburton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carol Van Ryzin
- Metabolic Medicine Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Tanya J Lehky
- EMG Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Christopher Zalewski
- Audiology Unit, Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD, USA
| | - Kelly A King
- Audiology Unit, Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD, USA
| | - Carmen C Brewer
- Audiology Unit, Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD, USA
| | - Audrey Thurm
- Neurodevelopmental and Behavioral Phenotyping Service, National Institute of Mental Health, NIH, Bethesda, MD, USA
| | - Joseph Snow
- Office of the Clinical Director, National Institute of Mental Health, NIH, Bethesda, MD, USA
| | - Flavia M Facio
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD, USA
- Invitae Corporation, San Francisco, CA, USA
| | - Narisu Narisu
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Lori L Bonnycastle
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Amy Swift
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Peter S Chines
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Jessica L Bell
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Suresh Mohan
- Department of Otolaryngology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Mary C Whitman
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sandra E Staffieri
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, and University of Melbourne, Melbourne, Victoria, Australia
- Department of Ophthalmology, Royal Children's Hospital, Parkville, Victoria, Australia
| | - James E Elder
- Department of Ophthalmology, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Joseph L Demer
- Stein Eye Institute and Departments of Ophthalmology, Neurology, and Bioengineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Alcy Torres
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatrics, Boston Medical Center, Boston University Aram V. Chobanian & Edward Avedisian School of Medicine, Boston, MA, USA
| | - Elza Rachid
- Department of Ophthalmology, American University of Beirut Medical Center, Beirut, Lebanon
| | - Christiane Al-Haddad
- Department of Ophthalmology, American University of Beirut Medical Center, Beirut, Lebanon
| | - Rose-Mary Boustany
- Pediatrics & Adolescent Medicine/Biochemistry & Molecular Genetics, American University of Beirut Medical Center, Beirut, Lebanon
| | - David A Mackey
- Lions Eye Institute, University of Western Australia, Perth, Australia
| | - Angela F Brady
- North West Thames Regional Genetics Service, Northwick Park Hospital, Harrow, UK
| | - María Fenollar-Cortés
- Unidad de Genética Clínica, Instituto de Medicina del Laboratorio. IdISSC, Hospital Clínico San Carlos, Madrid, Spain
| | - Melanie Fradin
- Service de Génétique Clinique, CHU Rennes, Centre Labellisé Anomalies du Développement, Rennes, France
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
- Center of Excellence for Neuropsychiatry, Vincent van Gogh Institute for Psychiatry, Venray, the Netherlands
| | - George W Padberg
- Department of Neurology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Salmo Raskin
- Centro de Aconselhamento e Laboratório Genetika, Curitiba, Paraná, Brazil
| | - Mario Teruo Sato
- Department of Ophthalmology & Otorhinolaryngology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Stuart H Orkin
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Stephen C J Parker
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Tessa A Hadlock
- Department of Otolaryngology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ethylin Wang Jabs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Francis S Collins
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Len A Pennacchio
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Irini Manoli
- Metabolic Medicine Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Elizabeth C Engle
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
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14
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Mahony CB, Copper L, Vrljicak P, Noyvert B, Constantinidou C, Browne S, Pan Y, Palles C, Ott S, Higgs MR, Monteiro R. Lineage skewing and genome instability underlie marrow failure in a zebrafish model of GATA2 deficiency. Cell Rep 2023; 42:112571. [PMID: 37256751 DOI: 10.1016/j.celrep.2023.112571] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 03/14/2023] [Accepted: 05/12/2023] [Indexed: 06/02/2023] Open
Abstract
Inherited bone marrow failure associated with heterozygous mutations in GATA2 predisposes toward hematological malignancies, but the mechanisms remain poorly understood. Here, we investigate the mechanistic basis of marrow failure in a zebrafish model of GATA2 deficiency. Single-cell transcriptomics and chromatin accessibility assays reveal that loss of gata2a leads to skewing toward the erythroid lineage at the expense of myeloid cells, associated with loss of cebpa expression and decreased PU.1 and CEBPA transcription factor accessibility in hematopoietic stem and progenitor cells (HSPCs). Furthermore, gata2a mutants show impaired expression of npm1a, the zebrafish NPM1 ortholog. Progressive loss of npm1a in HSPCs is associated with elevated levels of DNA damage in gata2a mutants. Thus, Gata2a maintains myeloid lineage priming through cebpa and protects against genome instability and marrow failure by maintaining expression of npm1a. Our results establish a potential mechanism underlying bone marrow failure in GATA2 deficiency.
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Affiliation(s)
- Christopher B Mahony
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Lucy Copper
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK; Cancer Research UK Birmingham Centre, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Pavle Vrljicak
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Boris Noyvert
- Centre for Computational Biology, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Chrystala Constantinidou
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK; Bioinformatics Research Technology Platform, University of Warwick, Coventry, UK
| | - Sofia Browne
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Yi Pan
- Centre for Computational Biology, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Claire Palles
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Sascha Ott
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK; Bioinformatics Research Technology Platform, University of Warwick, Coventry, UK
| | - Martin R Higgs
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Rui Monteiro
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
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15
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Jung MM, Shen S, Botten GA, Olender T, Katsumura KR, Johnson KD, Soukup AA, Liu P, Zhang Q, Jensvold ZD, Lewis PW, Beagrie RA, Low JK, Yang L, Mackay JP, Godley LA, Brand M, Xu J, Keles S, Bresnick EH. Pathogenic human variant that dislocates GATA2 zinc fingers disrupts hematopoietic gene expression and signaling networks. J Clin Invest 2023; 133:e162685. [PMID: 36809258 PMCID: PMC10065080 DOI: 10.1172/jci162685] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 02/16/2023] [Indexed: 02/23/2023] Open
Abstract
Although certain human genetic variants are conspicuously loss of function, decoding the impact of many variants is challenging. Previously, we described a patient with leukemia predisposition syndrome (GATA2 deficiency) with a germline GATA2 variant that inserts 9 amino acids between the 2 zinc fingers (9aa-Ins). Here, we conducted mechanistic analyses using genomic technologies and a genetic rescue system with Gata2 enhancer-mutant hematopoietic progenitor cells to compare how GATA2 and 9aa-Ins function genome-wide. Despite nuclear localization, 9aa-Ins was severely defective in occupying and remodeling chromatin and regulating transcription. Variation of the inter-zinc finger spacer length revealed that insertions were more deleterious to activation than repression. GATA2 deficiency generated a lineage-diverting gene expression program and a hematopoiesis-disrupting signaling network in progenitors with reduced granulocyte-macrophage colony-stimulating factor (GM-CSF) and elevated IL-6 signaling. As insufficient GM-CSF signaling caused pulmonary alveolar proteinosis and excessive IL-6 signaling promoted bone marrow failure and GATA2 deficiency patient phenotypes, these results provide insight into mechanisms underlying GATA2-linked pathologies.
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Affiliation(s)
- Mabel Minji Jung
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, and
| | - Siqi Shen
- Department of Biostatistics and Biomedical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Giovanni A. Botten
- Children’s Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Thomas Olender
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute–General Hospital, Ottawa, Ontario, Canada
| | - Koichi R. Katsumura
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, and
| | - Kirby D. Johnson
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, and
| | - Alexandra A. Soukup
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, and
| | - Peng Liu
- Department of Biostatistics and Biomedical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Qingzhou Zhang
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute–General Hospital, Ottawa, Ontario, Canada
| | - Zena D. Jensvold
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Peter W. Lewis
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Robert A. Beagrie
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jason K.K. Low
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Lihua Yang
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Joel P. Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Lucy A. Godley
- Section of Hematology/Oncology, The University of Chicago, Chicago, Illinois, USA
| | - Marjorie Brand
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Jian Xu
- Children’s Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Sunduz Keles
- Department of Biostatistics and Biomedical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Emery H. Bresnick
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, and
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16
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Man HSJ, Subramaniam N, Downs T, Sukumar AN, Saha AD, Nair R, Chen L, Teitelbaum D, Turgeon PJ, Ku KH, Tran E, de Perrot M, Marsden PA. Long noncoding RNA GATA2-AS1 augments endothelial Hypoxia Inducible Factor 1-α induction and regulates hypoxic signaling. J Biol Chem 2023; 299:103029. [PMID: 36806681 PMCID: PMC10148162 DOI: 10.1016/j.jbc.2023.103029] [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: 07/15/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 02/18/2023] Open
Abstract
Vascular endothelial cells form the inner cellular lining of blood vessels and have myriad physiologic functions including angiogenesis and response to hypoxia. We recently identified a set of endothelial cell (EC)-enriched long noncoding RNAs (lncRNAs) in differentiated human primary cell types and described the role of the STEEL lncRNA in angiogenic patterning. We sought to further understand the role of EC-enriched lncRNAs in physiologic adaptation of the vascular endothelium. In this work, we describe an abundant, cytoplasmic, and EC-enriched lncRNA, GATA2-AS1, that is divergently transcribed from the EC-enriched developmental regulator, GATA2. While GATA2-AS1 is largely co-expressed with GATA2 in ECs, GATA2-AS1 and GATA2 appear to be complementary rather than synergistic as they have mostly distinct target genes. Common single nucleotide variants (SNVs) in GATA2-AS1 exons are associated with early onset coronary artery disease (CAD) and decreased expression of GATA2-AS1 in endothelial cell lines. In most cells, HIF1-α is central to the transcriptional response to hypoxia, while in ECs, both HIF1-α and HIF2-α are required to coordinate an acute and chronic response respectively. In this setting, GATA2-AS1 contributes to the "HIF switch" and augments HIF1-α induction in acute hypoxia to regulate HIF1-α/ HIF2-α balance. In hypoxia, GATA2-AS1 orchestrates HIF1-α-dependent induction of the glycolytic pathway, and HIF1-α-independent maintenance of mitochondrial biogenesis. Similarly, GATA2-AS1 coordinates both metabolism and "tip/stalk" cell signaling to regulate angiogenesis in hypoxic ECs. Furthermore, we find that GATA2-AS1 expression patterns are perturbed in atherosclerotic disease. Together, these results define a role for GATA2-AS1 in the EC-specific response to hypoxia.
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Affiliation(s)
- H S Jeffrey Man
- Institute of Medical Science, Toronto, Ontario, Canada; Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, Toronto, Ontario, Canada; Department of Respirology, University Health Network, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Noeline Subramaniam
- Institute of Medical Science, Toronto, Ontario, Canada; Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Tiana Downs
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Aravin N Sukumar
- Institute of Medical Science, Toronto, Ontario, Canada; Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Aninda D Saha
- Institute of Medical Science, Toronto, Ontario, Canada; Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Ranju Nair
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Lucy Chen
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Daniel Teitelbaum
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Paul J Turgeon
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Kyung Ha Ku
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Eileen Tran
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Marc de Perrot
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, Toronto, Ontario, Canada; Division of Thoracic Surgery, Toronto General Hospital, Toronto, Ontario, Canada
| | - Philip A Marsden
- Institute of Medical Science, Toronto, Ontario, Canada; Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada.
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17
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Seong S, Vijayan V, Kim JH, Kim K, Kim I, Cherukula K, Park IK, Kim N. Nano-formulations for bone-specific delivery of siRNA for CrkII silencing-induced regulation of bone formation and resorption to maximize therapeutic potential for bone-related diseases. Biomater Sci 2023; 11:2581-2589. [PMID: 36794531 DOI: 10.1039/d2bm02038f] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
CrkII, a member of the adaptor protein family, is known to participate in bone homeostasis via the regulation of osteoclasts and osteoblasts. Therefore, silencing CrkII would beneficially impact the bone microenvironment. In this study, CrkII siRNA encapsulated by a bone-targeting peptide (AspSerSer)6-liposome was evaluated for its therapeutic applications using a receptor activator of nuclear factor kappa-B ligand (RANKL)-induced bone loss model. (AspSerSer)6-liposome-siCrkII maintained its gene-silencing ability in both osteoclasts and osteoblasts in vitro and significantly reduced osteoclast formation while increasing osteoblast differentiation in vitro. Fluorescence image analyses showed that the (AspSerSer)6-liposome-siCrkII was present largely in bone, where it remained present for up to 24 hours and was cleared by 48 hours, even when systemically administrated. Importantly, microcomputed-tomography revealed that bone loss induced by RANKL administration was recovered by systemic administration of (AspSerSer)6-liposome-siCrkII. Collectively, the findings of this study suggest that (AspSerSer)6-liposome-siCrkII is a promising therapeutic strategy for the development of treatments for bone diseases, as it overcomes the adverse effects derived from ubiquitous expression via bone-specific delivery of siRNA.
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Affiliation(s)
- Semun Seong
- Department of Pharmacology, Chonnam National University Medical School, Gwangju 61469, Republic of Korea. .,Hard-Tissue Biointerface Research Center, School of Dentistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Veena Vijayan
- Department of Biomedical Sciences and Center for Global Future Biomedical Scientists at Chonnam National University, Chonnam National University Medical School, Gwangju 61469, Republic of Korea.
| | - Jung Ha Kim
- Department of Pharmacology, Chonnam National University Medical School, Gwangju 61469, Republic of Korea. .,Hard-Tissue Biointerface Research Center, School of Dentistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Kabsun Kim
- Department of Pharmacology, Chonnam National University Medical School, Gwangju 61469, Republic of Korea.
| | - Inyoung Kim
- Department of Pharmacology, Chonnam National University Medical School, Gwangju 61469, Republic of Korea.
| | - Kondareddy Cherukula
- Department of Biomedical Sciences and Center for Global Future Biomedical Scientists at Chonnam National University, Chonnam National University Medical School, Gwangju 61469, Republic of Korea.
| | - In-Kyu Park
- Department of Biomedical Sciences and Center for Global Future Biomedical Scientists at Chonnam National University, Chonnam National University Medical School, Gwangju 61469, Republic of Korea.
| | - Nacksung Kim
- Department of Pharmacology, Chonnam National University Medical School, Gwangju 61469, Republic of Korea. .,Hard-Tissue Biointerface Research Center, School of Dentistry, Chonnam National University, Gwangju 61186, Republic of Korea
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18
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Vihinen M. Individual Genetic Heterogeneity. Genes (Basel) 2022; 13:genes13091626. [PMID: 36140794 PMCID: PMC9498725 DOI: 10.3390/genes13091626] [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: 08/12/2022] [Revised: 08/25/2022] [Accepted: 09/08/2022] [Indexed: 11/28/2022] Open
Abstract
Genetic variation has been widely covered in literature, however, not from the perspective of an individual in any species. Here, a synthesis of genetic concepts and variations relevant for individual genetic constitution is provided. All the different levels of genetic information and variation are covered, ranging from whether an organism is unmixed or hybrid, has variations in genome, chromosomes, and more locally in DNA regions, to epigenetic variants or alterations in selfish genetic elements. Genetic constitution and heterogeneity of microbiota are highly relevant for health and wellbeing of an individual. Mutation rates vary widely for variation types, e.g., due to the sequence context. Genetic information guides numerous aspects in organisms. Types of inheritance, whether Mendelian or non-Mendelian, zygosity, sexual reproduction, and sex determination are covered. Functions of DNA and functional effects of variations are introduced, along with mechanism that reduce and modulate functional effects, including TARAR countermeasures and intraindividual genetic conflict. TARAR countermeasures for tolerance, avoidance, repair, attenuation, and resistance are essential for life, integrity of genetic information, and gene expression. The genetic composition, effects of variations, and their expression are considered also in diseases and personalized medicine. The text synthesizes knowledge and insight on individual genetic heterogeneity and organizes and systematizes the central concepts.
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Affiliation(s)
- Mauno Vihinen
- Department of Experimental Medical Science, BMC B13, Lund University, SE-22184 Lund, Sweden
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19
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Jimenez E, Slevin CC, Song W, Chen Z, Frederickson SC, Gildea D, Wu W, Elkahloun AG, Ovcharenko I, Burgess SM. A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish. CELL GENOMICS 2022; 2. [PMID: 36212030 PMCID: PMC9540346 DOI: 10.1016/j.xgen.2022.100170] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Using adult zebrafish inner ears as a model for sensorineural regeneration, we ablated the mechanosensory receptors and characterized the single-cell epigenome and transcriptome at consecutive time points during hair cell regeneration. We utilized deep learning on the regeneration-induced open chromatin sequences and identified cell-specific transcription factor (TF) motif patterns. Enhancer activity correlated with gene expression and identified potential gene regulatory networks. A pattern of overlapping Sox- and Six-family TF gene expression and binding motifs was detected, suggesting a combinatorial program of TFs driving regeneration and cell identity. Pseudotime analysis of single-cell transcriptomic data suggested that support cells within the sensory epithelium changed cell identity to a “progenitor” cell population that could differentiate into hair cells. We identified a 2.6 kb DNA enhancer upstream of the sox2 promoter that, when deleted, showed a dominant phenotype that resulted in a hair-cell-regeneration-specific deficit in both the lateral line and adult inner ear. Jimenez et al. interrogate the epigenomic and transcriptomic landscape of regenerating adult zebrafish inner-ear sensory epithelia. They show that the support-cell population transitions to an intermediate “progenitor” cell state that becomes new hair cells, and they demonstrate that the cell fate decisions may be driven by the coordinate regulation and spatial co-binding of Sox and Six transcription factors. By functionally validating a predicted regeneration-responsive enhancer upstream of sox2, they show that precise timing of sox2 expression is critical for hearing regeneration in zebrafish.
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Affiliation(s)
- Erin Jimenez
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Claire C. Slevin
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Wei Song
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Zelin Chen
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Stephen C. Frederickson
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Derek Gildea
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Weiwei Wu
- Vaccine Immunology Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Abdel G. Elkahloun
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Ivan Ovcharenko
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Shawn M. Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
- Corresponding author
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20
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Downes DJ, Hughes JR. Natural and Experimental Rewiring of Gene Regulatory Regions. Annu Rev Genomics Hum Genet 2022; 23:73-97. [PMID: 35472292 DOI: 10.1146/annurev-genom-112921-010715] [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] [Indexed: 11/09/2022]
Abstract
The successful development and ongoing functioning of complex organisms depend on the faithful execution of the genetic code. A critical step in this process is the correct spatial and temporal expression of genes. The highly orchestrated transcription of genes is controlled primarily by cis-regulatory elements: promoters, enhancers, and insulators. The medical importance of this key biological process can be seen by the frequency with which mutations and inherited variants that alter cis-regulatory elements lead to monogenic and complex diseases and cancer. Here, we provide an overview of the methods available to characterize and perturb gene regulatory circuits. We then highlight mechanisms through which regulatory rewiring contributes to disease, and conclude with a perspective on how our understanding of gene regulation can be used to improve human health.
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Affiliation(s)
- Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom;
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom;
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom;
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21
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Johnson KD, Soukup AA, Bresnick EH. GATA2 deficiency elevates interferon regulatory factor-8 to subvert a progenitor cell differentiation program. Blood Adv 2022; 6:1464-1473. [PMID: 35008108 PMCID: PMC8905696 DOI: 10.1182/bloodadvances.2021006182] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/17/2021] [Indexed: 11/20/2022] Open
Abstract
Cell type-specific transcription factors control stem and progenitor cell transitions by establishing networks containing hundreds of genes and proteins. Network complexity renders it challenging to discover essential versus modulatory or redundant components. This scenario is exemplified by GATA2 regulation of hematopoiesis during embryogenesis. Loss of a far upstream Gata2 enhancer (-77) disrupts the GATA2-dependent transcriptome governing hematopoietic progenitor cell differentiation. The aberrant transcriptome includes the transcription factor interferon regulatory factor 8 (IRF8) and a host of innate immune regulators. Mutant progenitors lose the capacity to balance production of diverse hematopoietic progeny. To elucidate mechanisms, we asked if IRF8 is essential, contributory, or not required. Reducing Irf8, in the context of the -77 mutant allele, reversed granulocytic deficiencies and the excessive accumulation of dendritic cell committed progenitors. Despite many dysregulated components that control vital transcriptional, signaling, and immune processes, the aberrant elevation of a single transcription factor deconstructed the differentiation program.
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Affiliation(s)
| | - Alexandra A. Soukup
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Emery H. Bresnick
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI
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22
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You X, Zhou Y, Chang YI, Kong G, Ranheim EA, Johnson KD, Soukup AA, Bresnick EH, Zhang J. Gata2 +9.5 enhancer regulates adult hematopoietic stem cell self-renewal and T-cell development. Blood Adv 2022; 6:1095-1099. [PMID: 34516632 PMCID: PMC8864660 DOI: 10.1182/bloodadvances.2021004311] [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: 01/20/2021] [Accepted: 06/22/2021] [Indexed: 11/20/2022] Open
Abstract
Mammalian GATA2 gene encodes a dual zinc finger transcription factor, which is essential for hematopoietic stem cell (HSC) generation in the aorta, gonad, mesonephros (AGM) region, HSC self-renewal, and specification of progenitor cell fates. Previously, we demonstrated that Gata2 expression in AGM is controlled by its intronic +9.5 enhancer. Gata2 +9.5 deficiency removes the E-box motif and the GATA site and depletes fetal liver HSCs. However, whether this enhancer has an essential role in regulating adult hematopoiesis has not been established. Here, we evaluate Gata2 +9.5 enhancer function in adult hematopoiesis. +9.5+/- bone marrow cells displayed reduced T cell reconstitution in a competitive transplant assay. Donor-derived analysis demonstrated a previously unrecognized function of the +9.5 enhancer in T cell development at the lymphoid-primed multipotent progenitor stage. Moreover, +9.5+/- adult HSCs displayed increased apoptosis and reduced long-term self-renewal capability in comparison with wild-type (WT) HSCs. These phenotypes were more moderate than those of Gata2+/- HSCs. Consistent with the phenotypic characterization, Gata2 expression in +9.5+/- LSKs was moderately higher than that in Gata2+/- LSKs, but lower than that in WT LSKs. Our data suggest that +9.5 deficiency compromises, without completely abrogating, Gata2 expression in adult HSCs.
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Affiliation(s)
- Xiaona You
- McArdle Laboratory for Cancer Research
- Wisconsin Blood Cancer Research Institute, and
| | - Yun Zhou
- McArdle Laboratory for Cancer Research
- Wisconsin Blood Cancer Research Institute, and
| | | | | | - Erik A. Ranheim
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, WI; and
| | - Kirby D. Johnson
- Wisconsin Blood Cancer Research Institute, and
- Carbone Cancer Center, Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Alexandra A. Soukup
- Wisconsin Blood Cancer Research Institute, and
- Carbone Cancer Center, Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Emery H. Bresnick
- Wisconsin Blood Cancer Research Institute, and
- Carbone Cancer Center, Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Jing Zhang
- McArdle Laboratory for Cancer Research
- Wisconsin Blood Cancer Research Institute, and
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23
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Soukup AA, Matson DR, Liu P, Johnson KD, Bresnick EH. Conditionally pathogenic genetic variants of a hematopoietic disease-suppressing enhancer. SCIENCE ADVANCES 2021; 7:eabk3521. [PMID: 34890222 PMCID: PMC8664263 DOI: 10.1126/sciadv.abk3521] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/22/2021] [Indexed: 05/11/2023]
Abstract
Human genetic variants are classified on the basis of potential pathogenicity to guide clinical decisions. However, mechanistic uncertainties often preclude definitive categorization. Germline coding and enhancer variants within the hematopoietic regulator GATA2 create a bone marrow failure and leukemia predisposition. The conserved murine enhancer promotes hematopoietic stem cell (HSC) genesis, and a single-nucleotide human variant in an Ets motif attenuates chemotherapy-induced hematopoietic regeneration. We describe “conditionally pathogenic” (CP) enhancer motif variants that differentially affect hematopoietic development and regeneration. The Ets motif variant functioned autonomously in hematopoietic cells to disrupt hematopoiesis. Because an epigenetically silenced normal allele can exacerbate phenotypes of a pathogenic heterozygous variant, we engineered a bone marrow failure model harboring the Ets motif variant and a severe enhancer mutation on the second allele. Despite normal developmental hematopoiesis, regeneration in response to chemotherapy, inflammation, and a therapeutic HSC mobilizer was compromised. The CP paradigm informs mechanisms underlying phenotypic plasticity and clinical genetics.
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Affiliation(s)
- Alexandra A. Soukup
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Daniel R. Matson
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Peng Liu
- University of Wisconsin Carbone Cancer Center, Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Kirby D. Johnson
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Emery H. Bresnick
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
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24
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Heyes E, Schmidt L, Manhart G, Eder T, Proietti L, Grebien F. Identification of gene targets of mutant C/EBPα reveals a critical role for MSI2 in CEBPA-mutated AML. Leukemia 2021; 35:2526-2538. [PMID: 33623142 PMCID: PMC7611617 DOI: 10.1038/s41375-021-01169-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 01/12/2021] [Accepted: 01/28/2021] [Indexed: 01/31/2023]
Abstract
Mutations in the gene encoding the transcription factor CCAAT/enhancer-binding protein alpha (C/EBPα) occur in 10-15% of acute myeloid leukemia (AML). Frameshifts in the CEBPA N-terminus resulting in exclusive expression of a truncated p30 isoform represent the most prevalent type of CEBPA mutations in AML. C/EBPα p30 interacts with the epigenetic machinery, but it is incompletely understood how p30-induced changes cause leukemogenesis. We hypothesized that critical effector genes in CEBPA-mutated AML are dependent on p30-mediated dysregulation of the epigenome. We mapped p30-associated regulatory elements (REs) by ATAC-seq and ChIP-seq in a myeloid progenitor cell model for p30-driven AML that enables inducible RNAi-mediated knockdown of p30. Concomitant p30-dependent changes in gene expression were measured by RNA-seq. Integrative analysis identified 117 p30-dependent REs associated with 33 strongly down-regulated genes upon p30-knockdown. CRISPR/Cas9-mediated mutational disruption of these genes revealed the RNA-binding protein MSI2 as a critical p30-target. MSI2 knockout in p30-driven murine AML cells and in the CEBPA-mutated human AML cell line KO-52 caused proliferation arrest and terminal myeloid differentiation, and delayed leukemia onset in vivo. In summary, this work presents a comprehensive dataset of p30-dependent effects on epigenetic regulation and gene expression and identifies MSI2 as an effector of the C/EBPα p30 oncoprotein.
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Affiliation(s)
- Elizabeth Heyes
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria
| | - Luisa Schmidt
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria
| | - Gabriele Manhart
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria
| | - Thomas Eder
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria
| | - Ludovica Proietti
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria
| | - Florian Grebien
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria.
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25
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Human GATA2 mutations and hematologic disease: how many paths to pathogenesis? Blood Adv 2021; 4:4584-4592. [PMID: 32960960 DOI: 10.1182/bloodadvances.2020002953] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 08/21/2020] [Indexed: 01/19/2023] Open
Abstract
The surge of human genetic information, enabled by increasingly facile and economically feasible genomic technologies, has accelerated discoveries on the relationship of germline genetic variation to hematologic diseases. For example, germline variation in GATA2, encoding a vital transcriptional regulator of multilineage hematopoiesis, creates a predisposition to bone marrow failure and acute myeloid leukemia termed GATA2 deficiency syndrome. More than 300 GATA2 variants representing missense, truncating, and noncoding enhancer mutations have been documented. Although these variants can diminish GATA2 expression and/or function, the functional ramifications of many variants are unknown. Studies using genetic rescue and knockin mouse systems have established that GATA2 mutations differentially affect molecular processes in distinct target genes and within a single target cell. Considering that target genes for a transcription factor can differ in sensitivity to altered levels of the factor, and transcriptional mechanisms are often cell type specific, the context-dependent consequences of GATA2 mutations in experimental systems portend the complex phenotypes and interindividual variation of GATA2 deficiency syndrome. This review documents GATA2 human genetics and the state of efforts to traverse from physiological insights to pathogenic mechanisms.
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26
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Clark JF, Dinsmore CJ, Soriano P. A most formidable arsenal: genetic technologies for building a better mouse. Genes Dev 2021; 34:1256-1286. [PMID: 33004485 PMCID: PMC7528699 DOI: 10.1101/gad.342089.120] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this review, Clark et al. summarize the history of mice in genetic studies and the development of classic approaches to genome modification, and how they have been used and improved in recent years. They also discuss the recent surge of nuclease-mediated techniques and how they are changing the field of mouse genetics. The mouse is one of the most widely used model organisms for genetic study. The tools available to alter the mouse genome have developed over the preceding decades from forward screens to gene targeting in stem cells to the recent influx of CRISPR approaches. In this review, we first consider the history of mice in genetic study, the development of classic approaches to genome modification, and how such approaches have been used and improved in recent years. We then turn to the recent surge of nuclease-mediated techniques and how they are changing the field of mouse genetics. Finally, we survey common classes of alleles used in mice and discuss how they might be engineered using different methods.
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Affiliation(s)
- James F Clark
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mt. Sinai, New York, New York 10029, USA
| | - Colin J Dinsmore
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mt. Sinai, New York, New York 10029, USA
| | - Philippe Soriano
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mt. Sinai, New York, New York 10029, USA
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27
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Johnson KD, Conn DJ, Shishkova E, Katsumura KR, Liu P, Shen S, Ranheim EA, Kraus SG, Wang W, Calvo KR, Hsu AP, Holland SM, Coon JJ, Keles S, Bresnick EH. Constructing and deconstructing GATA2-regulated cell fate programs to establish developmental trajectories. J Exp Med 2021; 217:151996. [PMID: 32736380 PMCID: PMC7596813 DOI: 10.1084/jem.20191526] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 02/08/2020] [Accepted: 06/18/2020] [Indexed: 12/13/2022] Open
Abstract
Stem and progenitor cell fate transitions constitute key decision points in organismal development that enable access to a developmental path or actively preclude others. Using the hematopoietic system, we analyzed the relative importance of cell fate–promoting mechanisms versus negating fate-suppressing mechanisms to engineer progenitor cells with multilineage differentiation potential. Deletion of the murine Gata2−77 enhancer, with a human equivalent that causes leukemia, downregulates the transcription factor GATA2 and blocks progenitor differentiation into erythrocytes, megakaryocytes, basophils, and granulocytes, but not macrophages. Using multiomics and single-cell analyses, we demonstrated that the enhancer orchestrates a balance between pro- and anti-fate circuitry in single cells. By increasing GATA2 expression, the enhancer instigates a fate-promoting mechanism while abrogating an innate immunity–linked, fate-suppressing mechanism. During embryogenesis, the suppressing mechanism dominated in enhancer mutant progenitors, thus yielding progenitors with a predominant monocytic differentiation potential. Coordinating fate-promoting and -suppressing circuits therefore averts deconstruction of a multifate system into a monopotent system and maintains critical progenitor heterogeneity and functionality.
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Affiliation(s)
- Kirby D Johnson
- University of Wisconsin-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Daniel J Conn
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Koichi R Katsumura
- University of Wisconsin-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Peng Liu
- University of Wisconsin Carbone Cancer Center, Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Siqi Shen
- Department of Statistics, University of Wisconsin, Madison, WI
| | - Erik A Ranheim
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Sean G Kraus
- University of Wisconsin-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Weixin Wang
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD
| | - Katherine R Calvo
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD
| | - Amy P Hsu
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Joshua J Coon
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Sunduz Keles
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Emery H Bresnick
- University of Wisconsin-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI
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28
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Begeman IJ, Shin K, Osorio-Méndez D, Kurth A, Lee N, Chamberlain TJ, Pelegri FJ, Kang J. Decoding an organ regeneration switch by dissecting cardiac regeneration enhancers. Development 2020; 147:226055. [PMID: 33246928 DOI: 10.1242/dev.194019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 11/13/2020] [Indexed: 12/16/2022]
Abstract
Heart regeneration in regeneration-competent organisms can be accomplished through the remodeling of gene expression in response to cardiac injury. This dynamic transcriptional response relies on the activities of tissue regeneration enhancer elements (TREEs); however, the mechanisms underlying TREEs are poorly understood. We dissected a cardiac regeneration enhancer in zebrafish to elucidate the mechanisms governing spatiotemporal gene expression during heart regeneration. Cardiac lepb regeneration enhancer (cLEN) exhibits dynamic, regeneration-dependent activity in the heart. We found that multiple injury-activated regulatory elements are distributed throughout the enhancer region. This analysis also revealed that cardiac regeneration enhancers are not only activated by injury, but surprisingly, they are also actively repressed in the absence of injury. Our data identified a short (22 bp) DNA element containing a key repressive element. Comparative analysis across Danio species indicated that the repressive element is conserved in closely related species. The repression mechanism is not operational during embryogenesis and emerges when the heart begins to mature. Incorporating both activation and repression components into the mechanism of tissue regeneration constitutes a new paradigm that might be extrapolated to other regeneration scenarios.
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Affiliation(s)
- Ian J Begeman
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Kwangdeok Shin
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Daniel Osorio-Méndez
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Andrew Kurth
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Nutishia Lee
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Francisco J Pelegri
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Junsu Kang
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA.,UW Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
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29
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Liu P, Soukup AA, Bresnick EH, Dewey CN, Keleş S. PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments. Genome Res 2020; 30:1655-1666. [PMID: 32958497 PMCID: PMC7605252 DOI: 10.1101/gr.252445.119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 08/27/2020] [Indexed: 11/25/2022]
Abstract
Publicly available RNA-seq data is routinely used for retrospective analysis to elucidate new biology. Novel transcript discovery enabled by joint analysis of large collections of RNA-seq data sets has emerged as one such analysis. Current methods for transcript discovery rely on a '2-Step' approach where the first step encompasses building transcripts from individual data sets, followed by the second step that merges predicted transcripts across data sets. To increase the power of transcript discovery from large collections of RNA-seq data sets, we developed a novel '1-Step' approach named Pooling RNA-seq and Assembling Models (PRAM) that builds transcript models from pooled RNA-seq data sets. We demonstrate in a computational benchmark that 1-Step outperforms 2-Step approaches in predicting overall transcript structures and individual splice junctions, while performing competitively in detecting exonic nucleotides. Applying PRAM to 30 human ENCODE RNA-seq data sets identified unannotated transcripts with epigenetic and RAMPAGE signatures similar to those of recently annotated transcripts. In a case study, we discovered and experimentally validated new transcripts through the application of PRAM to mouse hematopoietic RNA-seq data sets. We uncovered new transcripts that share a differential expression pattern with a neighboring gene Pik3cg implicated in human hematopoietic phenotypes, and we provided evidence for the conservation of this relationship in human. PRAM is implemented as an R/Bioconductor package.
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Affiliation(s)
- Peng Liu
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Alexandra A Soukup
- Department of Cell and Regenerative Biology, Wisconsin Blood Cancer Research Institute, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53705, USA
| | - Emery H Bresnick
- Department of Cell and Regenerative Biology, Wisconsin Blood Cancer Research Institute, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53705, USA
| | - Colin N Dewey
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53706, USA.,Department of Computer Sciences, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Sündüz Keleş
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53706, USA.,Department of Statistics, University of Wisconsin, Madison, Wisconsin 53706, USA
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30
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Abstract
Regeneration is the process by which organisms replace lost or damaged tissue, and regenerative capacity can vary greatly among species, tissues and life stages. Tissue regeneration shares certain hallmarks of embryonic development, in that lineage-specific factors can be repurposed upon injury to initiate morphogenesis; however, many differences exist between regeneration and embryogenesis. Recent studies of regenerating tissues in laboratory model organisms - such as acoel worms, frogs, fish and mice - have revealed that chromatin structure, dedicated enhancers and transcriptional networks are regulated in a context-specific manner to control key gene expression programmes. A deeper mechanistic understanding of the gene regulatory networks of regeneration pathways might ultimately enable their targeted reactivation as a means to treat human injuries and degenerative diseases. In this Review, we consider the regeneration of body parts across a range of tissues and species to explore common themes and potentially exploitable elements.
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Affiliation(s)
- Joseph A Goldman
- Department of Biological Chemistry and Pharmacology, Ohio State University, Columbus, OH, USA.
| | - Kenneth D Poss
- Regeneration Next, Duke University, Durham, NC, USA.
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA.
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31
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The Role of Noncoding Variants in Heritable Disease. Trends Genet 2020; 36:880-891. [PMID: 32741549 DOI: 10.1016/j.tig.2020.07.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 12/26/2022]
Abstract
The genetic basis of disease has largely focused on coding regions. However, it has become clear that a large proportion of the noncoding genome is functional and harbors genetic variants that contribute to disease etiology. Here, we review recent examples of inherited noncoding alterations that are responsible for Mendelian disorders or act to influence complex traits. We explore both rare and common genetic variants and discuss the wide range of mechanisms by which they affect gene regulation to promote disease. We also debate the challenges and progress associated with identifying and interpreting the functional and clinical significance of genetic variation in the context of the noncoding regulatory landscape.
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32
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van Lier YF, de Bree GJ, Jonkers RE, Roelofs JJTH, Ten Berge IJM, Rutten CE, Nur E, Kuijpers TW, Hazenberg MD, Zeerleder SS. Allogeneic hematopoietic cell transplantation in the management of GATA2 deficiency and pulmonary alveolar proteinosis. Clin Immunol 2020; 218:108522. [PMID: 32682923 DOI: 10.1016/j.clim.2020.108522] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 06/29/2020] [Accepted: 06/29/2020] [Indexed: 12/17/2022]
Abstract
Human hematopoiesis is critically dependent on the transcription factor GATA2. Patients with GATA2 deficiency typically present with myelodysplastic syndrome, reduced numbers of monocytes, NK cells and B cells, and/or opportunistic infections. Here, we present two families that harbor distinct GATA2 mutations with highly variable onset and course of disease. We discuss the use of allogeneic hematopoietic cell transplantation in these patients, especially as treatment for pulmonary alveolar proteinosis.
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Affiliation(s)
- Yannouck F van Lier
- Department of Experimental Immunology, Amsterdam Infection & Immunity Institute (AII), Cancer Center Amsterdam (CCA), Amsterdam UMC location AMC, University of Amsterdam, 1105AZ Amsterdam, The Netherlands; Department of Hematology, Amsterdam UMC location AMC, University of Amsterdam, 1105AZ Amsterdam, The Netherlands
| | - Godelieve J de Bree
- Department of Infectious Diseases, Amsterdam UMC Location AMC, University of Amsterdam, 1105AZ Amsterdam, The Netherlands
| | - René E Jonkers
- Department of Respiratory Medicine, Amsterdam UMC location AMC, University of Amsterdam, 1105AZ Amsterdam, The Netherlands
| | - Joris J T H Roelofs
- Department of Pathology, Amsterdam UMC location AMC, University of Amsterdam, 1105AZ Amsterdam, The Netherlands
| | - Ineke J M Ten Berge
- Department of Experimental Immunology, Amsterdam Infection & Immunity Institute (AII), Cancer Center Amsterdam (CCA), Amsterdam UMC location AMC, University of Amsterdam, 1105AZ Amsterdam, The Netherlands; Department of Internal Medicine, Amsterdam UMC location AMC, University of Amsterdam, 1105AZ Amsterdam, The Netherlands
| | - Caroline E Rutten
- Department of Hematology, Amsterdam UMC location AMC, University of Amsterdam, 1105AZ Amsterdam, The Netherlands
| | - Erfan Nur
- Department of Hematology, Amsterdam UMC location AMC, University of Amsterdam, 1105AZ Amsterdam, The Netherlands
| | - Taco W Kuijpers
- Emma Children's Hospital, Amsterdam UMC location AMC, University of Amsterdam, 1105AZ Amsterdam, The Netherlands; Department of Blood Cell Research, Sanquin Research, 1066 CX Amsterdam, The Netherlands
| | - Mette D Hazenberg
- Department of Hematology, Amsterdam UMC location AMC, University of Amsterdam, 1105AZ Amsterdam, The Netherlands; Department of Hematopoiesis, Sanquin Research, 1066 CX Amsterdam, The Netherlands
| | - Sacha S Zeerleder
- Department of Immunopathology, Sanquin Research, 1066 CX Amsterdam, The Netherlands; Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, Switzerland and Department for BioMedical Research, University of Bern, 3010 Bern, Switzerland.
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33
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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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Ray S, Chee L, Matson DR, Palermo NY, Bresnick EH, Hewitt KJ. Sterile α-motif domain requirement for cellular signaling and survival. J Biol Chem 2020; 295:7113-7125. [PMID: 32241909 PMCID: PMC7242717 DOI: 10.1074/jbc.ra119.011895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 04/01/2020] [Indexed: 01/21/2023] Open
Abstract
Hundreds of sterile α-motif (SAM) domains have predicted structural similarities and are reported to bind proteins, lipids, or RNAs. However, the majority of these domains have not been analyzed functionally. Previously, we demonstrated that a SAM domain-containing protein, SAMD14, promotes SCF/proto-oncogene c-Kit (c-Kit) signaling, erythroid progenitor function, and erythrocyte regeneration. Deletion of a Samd14 enhancer (Samd14-Enh), occupied by GATA2 and SCL/TAL1 transcription factors, reduces SAMD14 expression in bone marrow and spleen and is lethal in a hemolytic anemia mouse model. To rigorously establish whether Samd14-Enh deletion reduces anemia-dependent c-Kit signaling by lowering SAMD14 levels, we developed a genetic rescue assay in murine Samd14-Enh-/- primary erythroid precursor cells. SAMD14 expression at endogenous levels rescued c-Kit signaling. The conserved SAM domain was required for SAMD14 to increase colony-forming activity, c-Kit signaling, and progenitor survival. To elucidate the molecular determinants of SAM domain function in SAMD14, we substituted its SAM domain with distinct SAM domains predicted to be structurally similar. The chimeras were less effective than SAMD14 itself in rescuing signaling, survival, and colony-forming activities. Thus, the SAMD14 SAM domain has attributes that are distinct from other SAM domains and underlie SAMD14 function as a regulator of cellular signaling and erythrocyte regeneration.
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Affiliation(s)
- Suhita Ray
- Department of Genetics, Cell Biology and Anatomy, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Linda Chee
- Department of Genetics, Cell Biology and Anatomy, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Daniel R Matson
- University of Wisconsin-Madison Blood Research Program, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53705
| | - Nick Y Palermo
- Holland Computing Center, University of Nebraska-Lincoln, Lincoln, Nebraska 68588
| | - Emery H Bresnick
- University of Wisconsin-Madison Blood Research Program, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53705
| | - Kyle J Hewitt
- Department of Genetics, Cell Biology and Anatomy, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68198
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35
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Soukup AA, Bresnick EH. GATA2 +9.5 enhancer: from principles of hematopoiesis to genetic diagnosis in precision medicine. Curr Opin Hematol 2020; 27:163-171. [PMID: 32205587 PMCID: PMC7331797 DOI: 10.1097/moh.0000000000000576] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW By establishing mechanisms that deliver oxygen to sustain cells and tissues, fight life-threatening pathogens and harness the immune system to eradicate cancer cells, hematopoietic stem and progenitor cells (HSPCs) are vital in health and disease. The cell biological framework for HSPC generation has been rigorously developed, yet recent single-cell transcriptomic analyses have unveiled permutations of the hematopoietic hierarchy that differ considerably from the traditional roadmap. Deploying mutants that disrupt specific steps in hematopoiesis constitutes a powerful strategy for deconvoluting the complex cell biology. It is striking that a single transcription factor, GATA2, is so crucial for HSPC generation and function, and therefore it is instructive to consider mechanisms governing GATA2 expression and activity. The present review focuses on an essential GATA2 enhancer (+9.5) and how +9.5 mutants inform basic and clinical/translational science. RECENT FINDINGS +9.5 is essential for HSPC generation and function during development and hematopoietic regeneration. Human +9.5 mutations cause immunodeficiency, myelodysplastic syndrome, and acute myeloid leukemia. Qualitatively and quantitatively distinct contributions of +9.5 cis-regulatory elements confer context-dependent enhancer activity. The discovery of +9.5 and its mutant alleles spawned fundamental insights into hematopoiesis, and given its role to suppress blood disease emergence, clinical centers test for mutations in this sequence to diagnose the cause of enigmatic cytopenias. SUMMARY Multidisciplinary approaches to discover and understand cis-regulatory elements governing expression of key regulators of hematopoiesis unveil biological and mechanistic insights that provide the logic for innovating clinical applications.
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36
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Cavalcante de Andrade Silva M, Katsumura KR, Mehta C, Velloso EDRP, Bresnick EH, Godley LA. Breaking the spatial constraint between neighboring zinc fingers: a new germline mutation in GATA2 deficiency syndrome. Leukemia 2020; 35:264-268. [PMID: 32286542 DOI: 10.1038/s41375-020-0820-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/18/2020] [Accepted: 03/27/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Marcela Cavalcante de Andrade Silva
- Serviço de Hematologia, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, BR Av. Dr. Eneas de Carvalho 155, Cerqueira César, 01246-000, São Paulo, SP, Brazil.,Section of Hematology/Oncology and Center for Clinical Cancer Genetics, The University of Chicago, Chicago, IL, USA
| | - Koichi R Katsumura
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Charu Mehta
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Elvira D R P Velloso
- Serviço de Hematologia, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, BR Av. Dr. Eneas de Carvalho 155, Cerqueira César, 01246-000, São Paulo, SP, Brazil
| | - Emery H Bresnick
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
| | - Lucy A Godley
- Section of Hematology/Oncology and Center for Clinical Cancer Genetics, The University of Chicago, Chicago, IL, USA.
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37
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Rodriguez AM, Kang J. Regeneration enhancers: Starting a journey to unravel regulatory events in tissue regeneration. Semin Cell Dev Biol 2020; 97:47-54. [PMID: 30953740 PMCID: PMC6783330 DOI: 10.1016/j.semcdb.2019.04.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 03/19/2019] [Accepted: 04/02/2019] [Indexed: 12/16/2022]
Abstract
Regeneration, an ability to replace lost body parts, is widespread across animal species. While mammals poorly regenerate most tissues, teleost fish and urodele amphibians possess remarkable regenerative capacity. Earlier work demonstrated that genes driving regeneration are evolutionarily conserved, indicating that a key factor in diverse tissue regeneration is not the presence or absence of regeneration-driving genes but the mechanisms controlling activation of these genes after injury. Thus, understanding the regulatory events of tissue regeneration could provide the means for unlocking latent capacities for tissue regeneration. After injury, cells undergo extensive epigenetic changes to establish new transcriptional programs for tissue regeneration. Gene transcription in eukaryotes is a complicated process that requires specific interactions between trans-acting regulators and cis-regulatory DNA elements. Among cis-regulatory elements, enhancers are essential to control precise gene expression. Recently, multiple regeneration/injury-associated enhancers have been identified in several model organisms. In this review, we highlight recently discovered regeneration/injury enhancers and their specific characteristics. We also discuss how abnormal regulation of regeneration enhancers influences animal development and physiology. Investigation of regeneration enhancers potentially allows us to begin understanding the fundamental biology of tissue regeneration and inspires new solutions for manipulating regenerative ability.
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Affiliation(s)
- Anjelica M Rodriguez
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, 53705, USA
| | - Junsu Kang
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, 53705, USA.
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38
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Shimizu R, Yamamoto M. Quantitative and qualitative impairments in GATA2 and myeloid neoplasms. IUBMB Life 2019; 72:142-150. [PMID: 31675473 DOI: 10.1002/iub.2188] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 10/07/2019] [Indexed: 12/27/2022]
Abstract
GATA2 is a key transcription factor critical for hematopoietic cell development. During the past decade, it became clear that heterozygous germline mutations in the GATA2 gene cause bone marrow failure and primary immunodeficiency syndrome, conditions that lead to a predisposition toward myeloid neoplasms, such as myelodysplastic syndrome, acute myeloid leukemia, and chronic myelomonocytic leukemia. Somatic mutations of the GATA2 gene are also involved in the pathogenesis of myeloid malignancies. Cases with GATA2 gene mutations are divided into two groups, resulting in either a quantitative deficiency or a qualitative defect in the GATA2 protein depending on the mutation position and type. In the former case, GATA2 mRNA expression from the mutant allele is markedly reduced or completely abrogated, and reduced GATA2 protein expression is involved in the pathogenesis. In the latter case, almost equal amounts of structurally abnormal and wildtype GATA2 proteins are predicted to be present and contribute to the pathogenesis. The development of mouse models of these human GATA2-related diseases has been undertaken, which naturally develop myeloid neoplasms.
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Affiliation(s)
- Ritsuko Shimizu
- Department of Molecular Hematology, Tohoku University Graduate School of Medicine, Sendai, Japan.,Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
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39
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Menendez-Gonzalez JB, Vukovic M, Abdelfattah A, Saleh L, Almotiri A, Thomas LA, Agirre-Lizaso A, Azevedo A, Menezes AC, Tornillo G, Edkins S, Kong K, Giles P, Anjos-Afonso F, Tonks A, Boyd AS, Kranc KR, Rodrigues NP. Gata2 as a Crucial Regulator of Stem Cells in Adult Hematopoiesis and Acute Myeloid Leukemia. Stem Cell Reports 2019; 13:291-306. [PMID: 31378673 PMCID: PMC6700503 DOI: 10.1016/j.stemcr.2019.07.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 07/05/2019] [Accepted: 07/05/2019] [Indexed: 12/12/2022] Open
Abstract
Subversion of transcription factor (TF) activity in hematopoietic stem/progenitor cells (HSPCs) leads to the development of therapy-resistant leukemic stem cells (LSCs) that drive fulminant acute myeloid leukemia (AML). Using a conditional mouse model where zinc-finger TF Gata2 was deleted specifically in hematopoietic cells, we show that knockout of Gata2 leads to rapid and complete cell-autonomous loss of adult hematopoietic stem cells. By using short hairpin RNAi to target GATA2, we also identify a requirement for GATA2 in human HSPCs. In Meis1a/Hoxa9-driven AML, deletion of Gata2 impedes maintenance and self-renewal of LSCs. Ablation of Gata2 enforces an LSC-specific program of enhanced apoptosis, exemplified by attenuation of anti-apoptotic factor BCL2, and re-instigation of myeloid differentiation--which is characteristically blocked in AML. Thus, GATA2 acts as a critical regulator of normal and leukemic stem cells and mediates transcriptional networks that may be exploited therapeutically to target key facets of LSC behavior in AML.
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MESH Headings
- Animals
- Apoptosis
- Cell Self Renewal
- Disease Models, Animal
- GATA2 Transcription Factor/antagonists & inhibitors
- GATA2 Transcription Factor/genetics
- GATA2 Transcription Factor/metabolism
- Hematopoiesis
- Hematopoietic Stem Cell Transplantation
- Hematopoietic Stem Cells/cytology
- Hematopoietic Stem Cells/metabolism
- Humans
- Kaplan-Meier Estimate
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/therapy
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Neoplastic Stem Cells/cytology
- Neoplastic Stem Cells/metabolism
- Proto-Oncogene Proteins c-bcl-2/metabolism
- RNA Interference
- RNA, Small Interfering/metabolism
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Affiliation(s)
| | - Milica Vukovic
- Centre for Hemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Ali Abdelfattah
- European Cancer Stem Cell Research Institute, Cardiff University, School of Biosciences, Cardiff CF24 4HQ, UK
| | - Lubaid Saleh
- European Cancer Stem Cell Research Institute, Cardiff University, School of Biosciences, Cardiff CF24 4HQ, UK
| | - Alhomidi Almotiri
- European Cancer Stem Cell Research Institute, Cardiff University, School of Biosciences, Cardiff CF24 4HQ, UK
| | - Leigh-Anne Thomas
- European Cancer Stem Cell Research Institute, Cardiff University, School of Biosciences, Cardiff CF24 4HQ, UK
| | - Aloña Agirre-Lizaso
- European Cancer Stem Cell Research Institute, Cardiff University, School of Biosciences, Cardiff CF24 4HQ, UK
| | - Aleksandra Azevedo
- Department of Hematology, Division of Cancer and Genetics, Cardiff University, School of Medicine, Cardiff CF14 4XW, UK
| | - Ana Catarina Menezes
- Department of Hematology, Division of Cancer and Genetics, Cardiff University, School of Medicine, Cardiff CF14 4XW, UK
| | - Giusy Tornillo
- European Cancer Stem Cell Research Institute, Cardiff University, School of Biosciences, Cardiff CF24 4HQ, UK
| | - Sarah Edkins
- Wales Gene Park and Wales Cancer Research Centre, Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF10 3XQ, UK
| | - Kay Kong
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Peter Giles
- Wales Gene Park and Wales Cancer Research Centre, Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF10 3XQ, UK
| | - Fernando Anjos-Afonso
- European Cancer Stem Cell Research Institute, Cardiff University, School of Biosciences, Cardiff CF24 4HQ, UK
| | - Alex Tonks
- Department of Hematology, Division of Cancer and Genetics, Cardiff University, School of Medicine, Cardiff CF14 4XW, UK
| | - Ashleigh S Boyd
- Department of Surgical Biotechnology, Division of Surgery and Interventional Science, Royal Free Hospital, University College London, London NW3 2PF, UK; Institute of Immunity and Transplantation, University College London, London NW3 2QG, UK
| | - Kamil R Kranc
- Centre for Hemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Neil P Rodrigues
- European Cancer Stem Cell Research Institute, Cardiff University, School of Biosciences, Cardiff CF24 4HQ, UK.
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40
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McReynolds LJ, Zhang Y, Yang Y, Tang J, Mulé M, Hsu AP, Townsley DM, West RR, Zhu J, Hickstein DD, Holland SM, Calvo KR, Hourigan CS. Rapid progression to AML in a patient with germline GATA2 mutation and acquired NRAS Q61K mutation. Leuk Res Rep 2019; 12:100176. [PMID: 31245276 PMCID: PMC6582196 DOI: 10.1016/j.lrr.2019.100176] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 05/28/2019] [Accepted: 06/07/2019] [Indexed: 12/16/2022] Open
Abstract
GATA2 deficiency syndrome is caused by autosomal dominant, heterozygous germline mutations with widespread effects on immune, pulmonary and vascular systems. Patients commonly develop hematological abnormalities including bone marrow failure, myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). We present a patient with GATA2 mutation and MDS who progressed to AML over four months. Whole exome and targeted deep sequencing identified a new p.Q61K NRAS mutation in the bone marrow at the time of AML development. Rapid development of AML is possible in the setting of germline GATA2 mutation despite stable MDS, supporting close monitoring and consideration of early allogeneic transplantation.
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Affiliation(s)
- Lisa J McReynolds
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Yubo Zhang
- DNA Sequencing and Genomics Core, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Yanqin Yang
- DNA Sequencing and Genomics Core, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Jingrong Tang
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Matthew Mulé
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Amy P Hsu
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Danielle M Townsley
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States.,MedImmune, Gaithersburg, MD, United States
| | - Robert R West
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Jun Zhu
- DNA Sequencing and Genomics Core, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Dennis D Hickstein
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Katherine R Calvo
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Christopher S Hourigan
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
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