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Ma F, Cao Y, Du H, Braikia FZ, Zong L, Ollikainen N, Bayer M, Qiu X, Park B, Roy R, Nandi S, Sarantopoulou D, Ziman A, Bianchi AH, Beerman I, Zhao K, Grosschedl R, Sen R. Three-dimensional chromatin reorganization regulates B cell development during ageing. Nat Cell Biol 2024; 26:991-1002. [PMID: 38866970 PMCID: PMC11178499 DOI: 10.1038/s41556-024-01424-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 04/16/2024] [Indexed: 06/14/2024]
Abstract
The contribution of three-dimensional genome organization to physiological ageing is not well known. Here we show that large-scale chromatin reorganization distinguishes young and old bone marrow progenitor (pro-) B cells. These changes result in increased interactions at the compartment level and reduced interactions within topologically associated domains (TADs). The gene encoding Ebf1, a key B cell regulator, switches from compartment A to B with age. Genetically reducing Ebf1 recapitulates some features of old pro-B cells. TADs that are most reduced with age contain genes important for B cell development, including the immunoglobulin heavy chain (Igh) locus. Weaker intra-TAD interactions at Igh correlate with altered variable (V), diversity (D) and joining (J) gene recombination. Our observations implicate three-dimensional chromatin reorganization as a major driver of pro-B cell phenotypes that impair B lymphopoiesis with age.
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Affiliation(s)
- Fei Ma
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Yaqiang Cao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | - Hansen Du
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Fatima Zohra Braikia
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Le Zong
- Epigenetics and Stem Cell Init, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Noah Ollikainen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Marc Bayer
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Xiang Qiu
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Bongsoo Park
- Epigenetics and Stem Cell Init, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Roshni Roy
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Satabdi Nandi
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Dimitra Sarantopoulou
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | | | - Aisha Haley Bianchi
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Isabel Beerman
- Epigenetics and Stem Cell Init, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | - Rudolf Grosschedl
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA.
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2
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Zhang X, Xia F, Zhang X, Blumenthal RM, Cheng X. C2H2 Zinc Finger Transcription Factors Associated with Hemoglobinopathies. J Mol Biol 2024; 436:168343. [PMID: 37924864 PMCID: PMC11185177 DOI: 10.1016/j.jmb.2023.168343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/23/2023] [Accepted: 10/30/2023] [Indexed: 11/06/2023]
Abstract
In humans, specific aberrations in β-globin results in sickle cell disease and β-thalassemia, symptoms of which can be ameliorated by increased expression of fetal globin (HbF). Two recent CRISPR-Cas9 screens, centered on ∼1500 annotated sequence-specific DNA binding proteins and performed in a human erythroid cell line that expresses adult hemoglobin, uncovered four groups of candidate regulators of HbF gene expression. They are (1) members of the nucleosome remodeling and deacetylase (NuRD) complex proteins that are already known for HbF control; (2) seven C2H2 zinc finger (ZF) proteins, including some (ZBTB7A and BCL11A) already known for directly silencing the fetal γ-globin genes in adult human erythroid cells; (3) a few other transcription factors of different structural classes that might indirectly influence HbF gene expression; and (4) DNA methyltransferase 1 (DNMT1) that maintains the DNA methylation marks that attract the MBD2-associated NuRD complex to DNA as well as associated histone H3 lysine 9 methylation. Here we briefly discuss the effects of these regulators, particularly C2H2 ZFs, in inducing HbF expression for treating β-hemoglobin disorders, together with recent advances in developing safe and effective small-molecule therapeutics for the regulation of this well-conserved hemoglobin switch.
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Affiliation(s)
- Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Fangfang Xia
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaotian Zhang
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center Houston, McGovern Medical School, Houston, TX 77030, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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3
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Rajendiran V, Devaraju N, Haddad M, Ravi NS, Panigrahi L, Paul J, Gopalakrishnan C, Wyman S, Ariudainambi K, Mahalingam G, Periyasami Y, Prasad K, George A, Sukumaran D, Gopinathan S, Pai AA, Nakamura Y, Balasubramanian P, Ramalingam R, Thangavel S, Velayudhan SR, Corn JE, Mackay JP, Marepally S, Srivastava A, Crossley M, Mohankumar KM. Base editing of key residues in the BCL11A-XL-specific zinc finger domains derepresses fetal globin expression. Mol Ther 2024; 32:663-677. [PMID: 38273654 PMCID: PMC10928131 DOI: 10.1016/j.ymthe.2024.01.023] [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: 04/28/2023] [Revised: 11/03/2023] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
BCL11A-XL directly binds and represses the fetal globin (HBG1/2) gene promoters, using 3 zinc-finger domains (ZnF4, ZnF5, and ZnF6), and is a potential target for β-hemoglobinopathy treatments. Disrupting BCL11A-XL results in derepression of fetal globin and high HbF, but also affects hematopoietic stem and progenitor cell (HSPC) engraftment and erythroid maturation. Intriguingly, neurodevelopmental patients with ZnF domain mutations have elevated HbF with normal hematological parameters. Inspired by this natural phenomenon, we used both CRISPR-Cas9 and base editing at specific ZnF domains and assessed the impacts on HbF production and hematopoietic differentiation. Generating indels in the various ZnF domains by CRISPR-Cas9 prevented the binding of BCL11A-XL to its site in the HBG1/2 promoters and elevated the HbF levels but affected normal hematopoiesis. Far fewer side effects were observed with base editing- for instance, erythroid maturation in vitro was near normal. However, we observed a modest reduction in HSPC engraftment and a complete loss of B cell development in vivo, presumably because current base editing is not capable of precisely recapitulating the mutations found in patients with BCL11A-XL-associated neurodevelopment disorders. Overall, our results reveal that disrupting different ZnF domains has different effects. Disrupting ZnF4 elevated HbF levels significantly while leaving many other erythroid target genes unaffected, and interestingly, disrupting ZnF6 also elevated HbF levels, which was unexpected because this region does not directly interact with the HBG1/2 promoters. This first structure/function analysis of ZnF4-6 provides important insights into the domains of BCL11A-XL that are required to repress fetal globin expression and provide framework for exploring the introduction of natural mutations that may enable the derepression of single gene while leaving other functions unaffected.
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Affiliation(s)
- Vignesh Rajendiran
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
| | - Nivedhitha Devaraju
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Mahdi Haddad
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Nithin Sam Ravi
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
| | - Lokesh Panigrahi
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Joshua Paul
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Chandrasekar Gopalakrishnan
- Department of Integrative Biology, School of Bioscience and Technology, Vellore Institute of Technology (VIT, Deemed to be University), Vellore, Tamil Nadu 632014, India
| | - Stacia Wyman
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94704, USA
| | | | - Gokulnath Mahalingam
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
| | - Yogapriya Periyasami
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
| | - Kirti Prasad
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Anila George
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
| | - Dhiyaneshwaran Sukumaran
- Department of Integrative Biology, School of Bioscience and Technology, Vellore Institute of Technology (VIT, Deemed to be University), Vellore, Tamil Nadu 632014, India
| | - Sandhiya Gopinathan
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
| | - Aswin Anand Pai
- Department of Haematology, Christian Medical College & Hospital, Vellore, Tamil Nadu 632 004, India
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | | | - Rajasekaran Ramalingam
- Department of Integrative Biology, School of Bioscience and Technology, Vellore Institute of Technology (VIT, Deemed to be University), Vellore, Tamil Nadu 632014, India
| | - Saravanabhavan Thangavel
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
| | - Shaji R Velayudhan
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Department of Haematology, Christian Medical College & Hospital, Vellore, Tamil Nadu 632 004, India
| | - Jacon E Corn
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94704, USA; Institute of Molecular Health Sciences, Department of Biology, Zurich, Switzerland
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Srujan Marepally
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
| | - Alok Srivastava
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Department of Haematology, Christian Medical College & Hospital, Vellore, Tamil Nadu 632 004, India
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Kumarasamypet M Mohankumar
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India.
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4
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Andresen AMS, Taylor RS, Grimholt U, Daniels RR, Sun J, Dobie R, Henderson NC, Martin SAM, Macqueen DJ, Fosse JH. Mapping the cellular landscape of Atlantic salmon head kidney by single cell and single nucleus transcriptomics. FISH & SHELLFISH IMMUNOLOGY 2024; 146:109357. [PMID: 38181891 DOI: 10.1016/j.fsi.2024.109357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/07/2024]
Abstract
Single-cell transcriptomics is the current gold standard for global gene expression profiling, not only in mammals and model species, but also in non-model fish species. This is a rapidly expanding field, creating a deeper understanding of tissue heterogeneity and the distinct functions of individual cells, making it possible to explore the complexities of immunology and gene expression on a highly resolved level. In this study, we compared two single cell transcriptomic approaches to investigate cellular heterogeneity within the head kidney of healthy farmed Atlantic salmon (Salmo salar). We compared 14,149 cell transcriptomes assayed by single cell RNA-seq (scRNA-seq) with 18,067 nuclei transcriptomes captured by single nucleus RNA-Seq (snRNA-seq). Both approaches detected eight major cell populations in common: granulocytes, heamatopoietic stem cells, erythrocytes, mononuclear phagocytes, thrombocytes, B cells, NK-like cells, and T cells. Four additional cell types, endothelial, epithelial, interrenal, and mesenchymal cells, were detected in the snRNA-seq dataset, but appeared to be lost during preparation of the single cell suspension submitted for scRNA-seq library generation. We identified additional heterogeneity and subpopulations within the B cells, T cells, and endothelial cells, and revealed developmental trajectories of heamatopoietic stem cells into differentiated granulocyte and mononuclear phagocyte populations. Gene expression profiles of B cell subtypes revealed distinct IgM and IgT-skewed resting B cell lineages and provided insights into the regulation of B cell lymphopoiesis. The analysis revealed eleven T cell sub-populations, displaying a level of T cell heterogeneity in salmon head kidney comparable to that observed in mammals, including distinct subsets of cd4/cd8-negative T cells, such as tcrγ positive, progenitor-like, and cytotoxic cells. Although snRNA-seq and scRNA-seq were both useful to resolve cell type-specific expression in the Atlantic salmon head kidney, the snRNA-seq pipeline was overall more robust in identifying several cell types and subpopulations. While scRNA-seq displayed higher levels of ribosomal and mitochondrial genes, snRNA-seq captured more transcription factor genes. However, only scRNA-seq-generated data was useful for cell trajectory inference within the myeloid lineage. In conclusion, this study systematically outlines the relative merits of scRNA-seq and snRNA-seq in Atlantic salmon, enhances understanding of teleost immune cell lineages, and provides a comprehensive list of markers for identifying major cell populations in the head kidney with significant immune relevance.
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Affiliation(s)
| | - Richard S Taylor
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Rose Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Jianxuan Sun
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Ross Dobie
- Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, United Kingdom
| | - Neil C Henderson
- Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, United Kingdom; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Samuel A M Martin
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Daniel J Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom.
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Matsumoto K, Okuyama K, Sidwell T, Yamashita M, Endo T, Satoh-Takayama N, Ohno H, Morio T, Rothenberg EV, Taniuchi I. A Bcl11b N797K variant isolated from an immunodeficient patient inhibits early thymocyte development in mice. Front Immunol 2024; 15:1363704. [PMID: 38495886 PMCID: PMC10940544 DOI: 10.3389/fimmu.2024.1363704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 02/20/2024] [Indexed: 03/19/2024] Open
Abstract
BCL11B is a transcription factor with six C2H2-type zinc-finger domains. Studies in mice have shown that Bcl11b plays essential roles in T cell development. Several germline heterozygous BCL11B variants have been identified in human patients with inborn errors of immunity (IEI) patients. Among these, two de novo mis-sense variants cause asparagine (N) to lysine (K) replacement in distinct zinc-finger domains, BCL11BN441K and BCL11BN807K. To elucidate the pathogenesis of the BCL11BN807K variant, we generated a mouse model of BCL11BN807K by inserting the corresponding mutation, Bcl11bN797K, into the mouse genome. In Bcl11b+/N797K mice, the proportion of immature CD4-CD8+ single-positive thymocytes was increased, and the development of invariant natural killer cells was severely inhibited in a T-cell-intrinsic manner. Under competitive conditions, γδT cell development was outcompeted by control cells. Bcl11bN797K/N797K mice died within one day of birth. Recipient mice reconstituted with Bcl11bN797K/N797K fetal liver cells nearly lacked CD4+CD8+ double-positive thymocytes, which was consistent with the lack of their emergence in culture from Bcl11bN797K/N797K fetal liver progenitors. Interestingly, Bcl11bN797K/N797K progenitors gave rise to aberrant c-Kit+ and CD44+ cells both in vivo and in vitro. The increase in the proportion of immature CD8 single-positive thymocytes in the Bcl11bN797K mutants is caused, in part, by the inefficient activation of the Cd4 gene due to the attenuated function of the two Cd4 enhancers via distinct mechanisms. Therefore, we conclude that immunodeficient patient-derived Bcl11bN797K mutant mice elucidated a novel role for Bcl11b in driving the appropriate transition of CD4-CD8- into CD4+CD8+ thymocytes.
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Affiliation(s)
- Kazuaki Matsumoto
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama Kanagawa, Japan
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kazuki Okuyama
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama Kanagawa, Japan
| | - Tom Sidwell
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Motoi Yamashita
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama Kanagawa, Japan
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takaho Endo
- Genome Platform, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama Kanagawa, Japan
| | - Naoko Satoh-Takayama
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama Kanagawa, Japan
| | - Hiroshi Ohno
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama Kanagawa, Japan
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ellen V. Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama Kanagawa, Japan
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Seigfried FA, Britsch S. The Role of Bcl11 Transcription Factors in Neurodevelopmental Disorders. BIOLOGY 2024; 13:126. [PMID: 38392344 PMCID: PMC10886639 DOI: 10.3390/biology13020126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/05/2024] [Accepted: 02/10/2024] [Indexed: 02/24/2024]
Abstract
Neurodevelopmental disorders (NDDs) comprise a diverse group of diseases, including developmental delay, autism spectrum disorder (ASD), intellectual disability (ID), and attention-deficit/hyperactivity disorder (ADHD). NDDs are caused by aberrant brain development due to genetic and environmental factors. To establish specific and curative therapeutic approaches, it is indispensable to gain precise mechanistic insight into the cellular and molecular pathogenesis of NDDs. Mutations of BCL11A and BCL11B, two closely related, ultra-conserved zinc-finger transcription factors, were recently reported to be associated with NDDs, including developmental delay, ASD, and ID, as well as morphogenic defects such as cerebellar hypoplasia. In mice, Bcl11 transcription factors are well known to orchestrate various cellular processes during brain development, for example, neural progenitor cell proliferation, neuronal migration, and the differentiation as well as integration of neurons into functional circuits. Developmental defects observed in both, mice and humans display striking similarities, suggesting Bcl11 knockout mice provide excellent models for analyzing human disease. This review offers a comprehensive overview of the cellular and molecular functions of Bcl11a and b and links experimental research to the corresponding NDDs observed in humans. Moreover, it outlines trajectories for future translational research that may help to better understand the molecular basis of Bcl11-dependent NDDs as well as to conceive disease-specific therapeutic approaches.
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Affiliation(s)
- Franziska Anna Seigfried
- Institute of Molecular and Cellular Anatomy, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Stefan Britsch
- Institute of Molecular and Cellular Anatomy, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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7
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Wang N, Wan R, Tang K. Transcriptional regulation in the development and dysfunction of neocortical projection neurons. Neural Regen Res 2024; 19:246-254. [PMID: 37488873 PMCID: PMC10503610 DOI: 10.4103/1673-5374.379039] [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: 01/29/2023] [Revised: 04/10/2023] [Accepted: 05/17/2023] [Indexed: 07/26/2023] Open
Abstract
Glutamatergic projection neurons generate sophisticated excitatory circuits to integrate and transmit information among different cortical areas, and between the neocortex and other regions of the brain and spinal cord. Appropriate development of cortical projection neurons is regulated by certain essential events such as neural fate determination, proliferation, specification, differentiation, migration, survival, axonogenesis, and synaptogenesis. These processes are precisely regulated in a tempo-spatial manner by intrinsic factors, extrinsic signals, and neural activities. The generation of correct subtypes and precise connections of projection neurons is imperative not only to support the basic cortical functions (such as sensory information integration, motor coordination, and cognition) but also to prevent the onset and progression of neurodevelopmental disorders (such as intellectual disability, autism spectrum disorders, anxiety, and depression). This review mainly focuses on the recent progress of transcriptional regulations on the development and diversity of neocortical projection neurons and the clinical relevance of the failure of transcriptional modulations.
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Affiliation(s)
- Ningxin Wang
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong Province, China
| | - Rong Wan
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong Province, China
| | - Ke Tang
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong Province, China
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8
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Zheng G, Orkin SH. Transcriptional Repressor BCL11A in Erythroid Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1459:199-215. [PMID: 39017845 DOI: 10.1007/978-3-031-62731-6_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
BCL11A, a zinc finger repressor, is a stage-specific transcription factor that controls the switch from fetal (HbF, α2γ2) to adult (HbA, α2β2) hemoglobin in erythroid cells. While BCL11A was known as a factor critical for B-lymphoid cell development, its relationship to erythroid cells and HbF arose through genome-wide association studies (GWAS). Subsequent work validated its role as a silencer of γ-globin gene expression in cultured cells and mice. Erythroid-specific loss of BCL11A rescues the phenotype of engineered sickle cell disease (SCD) mice, thereby suggesting that downregulation of BCL11A expression might be beneficial in patients with SCD and β-thalassemia. Common genetic variation in GWAS resides in an erythroid-specific enhancer within the BCL11A gene that is required for its own expression. CRISPR/Cas9 gene editing of the enhancer revealed a GATA-binding site that confers a large portion of its regulatory function. Disruption of the GATA site leads to robust HbF reactivation. Advancement of a guide RNA targeting the GATA-binding site in clinical trials has recently led to approval of first-in-man use of ex vivo CRISPR editing of hematopoietic stem/progenitor cells (HSPCs) as therapy of SCD and β-thalassemia. Future challenges include expanding access and infrastructure for delivery of genetic therapy to eligible patients, reducing potential toxicity and costs, exploring prospects for in vivo targeting of hematopoietic stem cells (HSCs), and developing small molecule drugs that impair function of BCL11A protein as an alternative option.
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Affiliation(s)
- Ge Zheng
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Harvard Medical School and HHMI, Boston, MA, USA
| | - Stuart H Orkin
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA.
- Harvard Medical School and HHMI, Boston, MA, USA.
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9
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Han W, Qiu HY, Sun S, Fu ZC, Wang GQ, Qian X, Wang L, Zhai X, Wei J, Wang Y, Guo YL, Cao GH, Ji RJ, Zhang YZ, Ma H, Wang H, Zhao M, Wu J, Bi L, Chen QB, Li Z, Yu L, Mou X, Yin H, Yang L, Chen J, Yang B, Zhang Y. Base editing of the HBG promoter induces potent fetal hemoglobin expression with no detectable off-target mutations in human HSCs. Cell Stem Cell 2023; 30:1624-1639.e8. [PMID: 37989316 DOI: 10.1016/j.stem.2023.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 09/13/2023] [Accepted: 10/24/2023] [Indexed: 11/23/2023]
Abstract
Reactivating silenced γ-globin expression through the disruption of repressive regulatory domains offers a therapeutic strategy for treating β-hemoglobinopathies. Here, we used transformer base editor (tBE), a recently developed cytosine base editor with no detectable off-target mutations, to disrupt transcription-factor-binding motifs in hematopoietic stem cells. By performing functional screening of six motifs with tBE, we found that directly disrupting the BCL11A-binding motif in HBG1/2 promoters triggered the highest γ-globin expression. Via a side-by-side comparison with other clinical and preclinical strategies using Cas9 nuclease or conventional BEs (ABE8e and hA3A-BE3), we found that tBE-mediated disruption of the BCL11A-binding motif at the HBG1/2 promoters triggered the highest fetal hemoglobin in healthy and β-thalassemia patient hematopoietic stem/progenitor cells while exhibiting no detectable DNA or RNA off-target mutations. Durable therapeutic editing by tBE persisted in repopulating hematopoietic stem cells, demonstrating that tBE-mediated editing in HBG1/2 promoters is a safe and effective strategy for treating β-hemoglobinopathies.
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Affiliation(s)
- Wenyan Han
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Hou-Yuan Qiu
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Shangwu Sun
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Zhi-Can Fu
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Center for Molecular Medicine, Children's Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Guo-Quan Wang
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Xiaowen Qian
- Department of Hematology and Oncology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Lijie Wang
- CorrectSequence Therapeutics, Shanghai 201210, China
| | - Xiaowen Zhai
- Department of Hematology and Oncology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Jia Wei
- Center for Molecular Medicine, Children's Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Yichuan Wang
- CorrectSequence Therapeutics, Shanghai 201210, China
| | - Yi-Lin Guo
- Center for Molecular Medicine, Children's Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Guo-Hua Cao
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Rui-Jin Ji
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Yi-Zhou Zhang
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Hongxia Ma
- CorrectSequence Therapeutics, Shanghai 201210, China
| | - Hongsheng Wang
- Department of Hematology and Oncology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Mingli Zhao
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jing Wu
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Lili Bi
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Qiu-Bing Chen
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Zifeng Li
- Department of Hematology and Oncology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Ling Yu
- Department of Hematology and Oncology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Xiaodun Mou
- CorrectSequence Therapeutics, Shanghai 201210, China
| | - Hao Yin
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Department of Pathology and Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China; TaiKang Centre for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China; State Key Laboratory of Virology, Wuhan University, Wuhan, China
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
| | - Jia Chen
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China; Shanghai Frontiers Science Center for Biomacromolecules and Precision Medicine, ShanghaiTech University, Shanghai 200031, China.
| | - Bei Yang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China; Shanghai Frontiers Science Center for Biomacromolecules and Precision Medicine, ShanghaiTech University, Shanghai 200031, China.
| | - Ying Zhang
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; State Key Laboratory of Virology, Wuhan University, Wuhan, China.
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10
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Zeng S, Lei S, Qu C, Wang Y, Teng S, Huang P. CRISPR/Cas-based gene editing in therapeutic strategies for beta-thalassemia. Hum Genet 2023; 142:1677-1703. [PMID: 37878144 DOI: 10.1007/s00439-023-02610-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 10/10/2023] [Indexed: 10/26/2023]
Abstract
Beta-thalassemia (β-thalassemia) is an autosomal recessive disorder caused by point mutations, insertions, and deletions in the HBB gene cluster, resulting in the underproduction of β-globin chains. The most severe type may demonstrate complications including massive hepatosplenomegaly, bone deformities, and severe growth retardation in children. Treatments for β-thalassemia include blood transfusion, splenectomy, and allogeneic hematopoietic stem cell transplantation (HSCT). However, long-term blood transfusions require regular iron removal therapy. For allogeneic HSCT, human lymphocyte antigen (HLA)-matched donors are rarely available, and acute graft-versus-host disease (GVHD) may occur after the transplantation. Thus, these conventional treatments are facing significant challenges. In recent years, with the advent and advancement of CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9) gene editing technology, precise genome editing has achieved encouraging successes in basic and clinical studies for treating various genetic disorders, including β-thalassemia. Target gene-edited autogeneic HSCT helps patients avoid graft rejection and GVHD, making it a promising curative therapy for transfusion-dependent β-thalassemia (TDT). In this review, we introduce the development and mechanisms of CRISPR/Cas9. Recent advances on feasible strategies of CRISPR/Cas9 targeting three globin genes (HBB, HBG, and HBA) and targeting cell selections for β-thalassemia therapy are highlighted. Current CRISPR-based clinical trials in the treatment of β-thalassemia are summarized, which are focused on γ-globin reactivation and fetal hemoglobin reproduction in hematopoietic stem cells. Lastly, the applications of other promising CRISPR-based technologies, such as base editing and prime editing, in treating β-thalassemia and the limitations of the CRISPR/Cas system in therapeutic applications are discussed.
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Affiliation(s)
- Shujun Zeng
- The Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, Jilin, People's Republic of China
| | - Shuangyin Lei
- The Second Norman Bethune Clinical College of Jilin University, Changchun, Jilin, People's Republic of China
| | - Chao Qu
- The First Norman Bethune Clinical College of Jilin University, Changchun, Jilin, People's Republic of China
| | - Yue Wang
- The Second Norman Bethune Clinical College of Jilin University, Changchun, Jilin, People's Republic of China
| | - Shuzhi Teng
- The Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, Jilin, People's Republic of China.
| | - Ping Huang
- The Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, Jilin, People's Republic of China.
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11
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Khan DMIO, Karmaus PWF, Bach A, Crawford RB, Kaminski NE. An in vitro model of human hematopoiesis identifies a regulatory role for the aryl hydrocarbon receptor. Blood Adv 2023; 7:6253-6265. [PMID: 37477592 PMCID: PMC10589788 DOI: 10.1182/bloodadvances.2023010169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/22/2023] [Accepted: 07/12/2023] [Indexed: 07/22/2023] Open
Abstract
In vitro models to study simultaneous development of different human immune cells and hematopoietic lineages are lacking. We identified and characterized, using single-cell methods, an in vitro stromal cell-free culture system of human hematopoietic stem and progenitor cell (HSPC) differentiation that allows concurrent development of multiple immune cell lineages. The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor influencing many biological processes in diverse cell types. Using this in vitro model, we found that AHR activation by the highly specific AHR ligand, 2,3,7,8-tetrachlorodibenzo-p-dioxin, drives differentiation of human umbilical cord blood-derived CD34+ HSPCs toward monocytes and granulocytes with a significant decrease in lymphoid and megakaryocyte lineage specification that may lead to reduced immune competence. To our knowledge, we also discovered for the first time, using single-cell modalities, that AHR activation decreased the expression of BCL11A and IRF8 in progenitor cells, which are critical genes involved in hematopoietic lineage specification processes at both transcriptomic and protein levels. Our in vitro model of hematopoiesis, coupled with single-cell tools, therefore allows for a better understanding of the role played by AHR in modulating hematopoietic differentiation.
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Affiliation(s)
- D M Isha Olive Khan
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI
| | - Peer W. F. Karmaus
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI
- National Institute of Environmental Health Sciences, Durham, NC
| | - Anthony Bach
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI
| | - Robert B. Crawford
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI
| | - Norbert E. Kaminski
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI
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12
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Zaunz S, De Smedt J, Lauwereins L, Cleuren L, Laffeber C, Bajaj M, Lebbink JHG, Marteijn JA, De Keersmaecker K, Verfaillie C. APEX1 Nuclease and Redox Functions are Both Essential for Adult Mouse Hematopoietic Stem and Progenitor Cells. Stem Cell Rev Rep 2023:10.1007/s12015-023-10550-0. [PMID: 37266894 PMCID: PMC10390635 DOI: 10.1007/s12015-023-10550-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2023] [Indexed: 06/03/2023]
Abstract
Self-renewal and differentiation of hematopoietic stem and progenitor cells (HSPCs) are carefully controlled by extrinsic and intrinsic factors, to ensure the lifelong process of hematopoiesis. Apurinic/apyrimidinic endonuclease 1 (APEX1) is a multifunctional protein implicated in DNA repair and transcriptional regulation. Although previous studies have emphasized the necessity of studying APEX1 in a lineage-specific context and its role in progenitor differentiation, no studies have assessed the role of APEX1, nor its two enzymatic domains, in supporting adult HSPC function. In this study, we demonstrated that complete loss of APEX1 from murine bone marrow HSPCs (induced by CRISPR/Cas9) caused severe hematopoietic failure following transplantation, as well as a HSPC expansion defect in culture conditions maintaining in vivo HSC functionality. Using specific inhibitors against either the nuclease or redox domains of APEX1 in combination with single cell transcriptomics (CITE-seq), we found that both APEX1 nuclease and redox domains are regulating mouse HSPCs, but through distinct underlying transcriptional changes. Inhibition of the APEX1 nuclease function resulted in loss of HSPCs accompanied by early activation of differentiation programs and enhanced lineage commitment. By contrast, inhibition of the APEX1 redox function significantly downregulated interferon-stimulated genes and regulons in expanding HSPCs and their progeny, resulting in dysfunctional megakaryocyte-biased HSPCs, as well as loss of monocytes and lymphoid progenitor cells. In conclusion, we demonstrate that APEX1 is a key regulator for adult regenerative hematopoiesis, and that the APEX1 nuclease and redox domains differently impact proliferating HSPCs.
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Affiliation(s)
- Samantha Zaunz
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, O&N IV Herestraat 49, 3000, Louvain, Belgium.
| | - Jonathan De Smedt
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, O&N IV Herestraat 49, 3000, Louvain, Belgium
- GlaxoSmithKline Biologicals SA, 1300, Wavre, Belgium
| | - Lukas Lauwereins
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, O&N IV Herestraat 49, 3000, Louvain, Belgium
| | - Lana Cleuren
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, O&N IV Herestraat 49, 3000, Louvain, Belgium
| | - Charlie Laffeber
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Manmohan Bajaj
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, O&N IV Herestraat 49, 3000, Louvain, Belgium
| | - Joyce H G Lebbink
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Radiotherapy, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Kim De Keersmaecker
- Laboratory for Disease Mechanisms in Cancer, Department of Oncology, KU Leuven, Louvain, Belgium
| | - Catherine Verfaillie
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, O&N IV Herestraat 49, 3000, Louvain, Belgium
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13
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Paschoudi K, Yannaki E, Psatha N. Precision Editing as a Therapeutic Approach for β-Hemoglobinopathies. Int J Mol Sci 2023; 24:ijms24119527. [PMID: 37298481 DOI: 10.3390/ijms24119527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/19/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Beta-hemoglobinopathies are the most common genetic disorders worldwide, caused by a wide spectrum of mutations in the β-globin locus, and associated with morbidity and early mortality in case of patient non-adherence to supportive treatment. Allogeneic transplantation of hematopoietic stem cells (allo-HSCT) used to be the only curative option, although the indispensable need for an HLA-matched donor markedly restricted its universal application. The evolution of gene therapy approaches made possible the ex vivo delivery of a therapeutic β- or γ- globin gene into patient-derived hematopoietic stem cells followed by the transplantation of corrected cells into myeloablated patients, having led to high rates of transfusion independence (thalassemia) or complete resolution of painful crises (sickle cell disease-SCD). Hereditary persistence of fetal hemoglobin (HPFH), a syndrome characterized by increased γ-globin levels, when co-inherited with β-thalassemia or SCD, converts hemoglobinopathies to a benign condition with mild clinical phenotype. The rapid development of precise genome editing tools (ZFN, TALENs, CRISPR/Cas9) over the last decade has allowed the targeted introduction of mutations, resulting in disease-modifying outcomes. In this context, genome editing tools have successfully been used for the introduction of HPFH-like mutations both in HBG1/HBG2 promoters or/and in the erythroid enhancer of BCL11A to increase HbF expression as an alternative curative approach for β-hemoglobinopathies. The current investigation of new HbF modulators, such as ZBTB7A, KLF-1, SOX6, and ZNF410, further expands the range of possible genome editing targets. Importantly, genome editing approaches have recently reached clinical translation in trials investigating HbF reactivation in both SCD and thalassemic patients. Showing promising outcomes, these approaches are yet to be confirmed in long-term follow-up studies.
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Affiliation(s)
- Kiriaki Paschoudi
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Gene and Cell Therapy Center, Hematology Clinic, George Papanikolaou Hospital, Exokhi, 57010 Thessaloniki, Greece
| | - Evangelia Yannaki
- Gene and Cell Therapy Center, Hematology Clinic, George Papanikolaou Hospital, Exokhi, 57010 Thessaloniki, Greece
- Department of Hematology, School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Nikoletta Psatha
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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14
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Gnanapragasam MN, Planutis A, Glassberg JA, Bieker JJ. Identification of a genomic DNA sequence that quantitatively modulates KLF1 transcription factor expression in differentiating human hematopoietic cells. Sci Rep 2023; 13:7589. [PMID: 37165057 PMCID: PMC10172341 DOI: 10.1038/s41598-023-34805-5] [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: 12/18/2022] [Accepted: 05/08/2023] [Indexed: 05/12/2023] Open
Abstract
The onset of erythropoiesis is under strict developmental control, with direct and indirect inputs influencing its derivation from the hematopoietic stem cell. A major regulator of this transition is KLF1/EKLF, a zinc finger transcription factor that plays a global role in all aspects of erythropoiesis. Here, we have identified a short, conserved enhancer element in KLF1 intron 1 that is important for establishing optimal levels of KLF1 in mouse and human cells. Chromatin accessibility of this site exhibits cell-type specificity and is under developmental control during the differentiation of human CD34+ cells towards the erythroid lineage. This site binds GATA1, SMAD1, TAL1, and ETV6. In vivo editing of this region in cell lines and primary cells reduces KLF1 expression quantitatively. However, we find that, similar to observations seen in pedigrees of families with KLF1 mutations, downstream effects are variable, suggesting that the global architecture of the site is buffered towards keeping the KLF1 genetic region in an active state. We propose that modification of intron 1 in both alleles is not equivalent to complete loss of function of one allele.
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Affiliation(s)
- M N Gnanapragasam
- Department of Cell, Developmental, and Regenerative Biology, Mount Sinai School of Medicine, One Gustave L. Levy Place, Box 1020, New York, NY, 10029, USA
- Department of Biological, Geological, and Environmental Sciences, Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH, USA
| | - A Planutis
- Department of Cell, Developmental, and Regenerative Biology, Mount Sinai School of Medicine, One Gustave L. Levy Place, Box 1020, New York, NY, 10029, USA
| | - J A Glassberg
- Department of Emergency Medicine, Hematology and Medical Oncology, Mount Sinai School of Medicine, New York, NY, USA
| | - J J Bieker
- Department of Cell, Developmental, and Regenerative Biology, Mount Sinai School of Medicine, One Gustave L. Levy Place, Box 1020, New York, NY, 10029, USA.
- Black Family Stem Cell Institute, Mount Sinai School of Medicine, New York, USA.
- Tisch Cancer Institute, Mount Sinai School of Medicine, New York, USA.
- Mindich Child Health and Development Institute, Mount Sinai School of Medicine, New York, NY, USA.
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15
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Yin J, Xie X, Quan Y, Wang Z, Liu S, Su Q, Che F, Wang L. RNA-seq analysis reveals candidate genes associated with proliferation, invasion, and migration in BCL11A knockdown B-NHL cell lines. Ann Hematol 2023:10.1007/s00277-023-05247-w. [PMID: 37148312 DOI: 10.1007/s00277-023-05247-w] [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: 12/05/2022] [Accepted: 04/25/2023] [Indexed: 05/08/2023]
Abstract
B-cell lymphoma/leukemia 11A (BCL11A) is highly expressed in B-cell non-Hodgkin lymphoma (B-NHL), blocks cell differentiation, and inhibits cell apoptosis. However, little is known about BCL11A in the proliferation, invasion, and migration of B-NHL cells. Here, we found increased expression of BCL11A in B-NHL patients and cell lines. Knockdown of BCL11A suppressed the proliferation, invasion, and migration of B-NHL cells in vitro and reduced tumor growth in vivo. RNA sequencing (RNA-seq) and KEGG pathway analysis demonstrated that BCL11A-targeted genes were significantly enriched in the PI3K/AKT signaling pathway, focal adhesion, and extracellular matrix (ECM)-receptor interaction (including COL4A1, COL4A2, FN1, SPP1), and SPP1 was the most significantly downregulated gene. qRT‒PCR, western blotting, and immunohistochemistry revealed that silencing BCL11A reduced the expression level of SPP1 in Raji cells. Our study suggested that high level of BCL11A may promote B-NHL proliferation, invasion, and migration, and the BCL11A-SPP1 regulatory axis may play an important role in Burkitt's lymphoma.
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Affiliation(s)
- Jiawei Yin
- Central Laboratory, Linyi People's Hospital, Shandong University, Linyi, Shandong, People's Republic of China
- Key Laboratory of Tumor Biology, Linyi, Shandong, People's Republic of China
- Key Laboratory for Translational Oncolgoy, Xuzhou Medical University, Xuzhou, Jiangsu, People's Republic of China
| | - Xiaoli Xie
- Central Laboratory, Linyi People's Hospital, Shandong University, Linyi, Shandong, People's Republic of China
- Key Laboratory of Tumor Biology, Linyi, Shandong, People's Republic of China
- Key Laboratory for Translational Oncolgoy, Xuzhou Medical University, Xuzhou, Jiangsu, People's Republic of China
| | - Yanchun Quan
- Central Laboratory, Linyi People's Hospital, Shandong University, Linyi, Shandong, People's Republic of China
- Key Laboratory of Tumor Biology, Linyi, Shandong, People's Republic of China
- Key Laboratory for Translational Oncolgoy, Xuzhou Medical University, Xuzhou, Jiangsu, People's Republic of China
| | - Zhiqiang Wang
- Central Laboratory, Linyi People's Hospital, Shandong University, Linyi, Shandong, People's Republic of China
- Key Laboratory of Tumor Biology, Linyi, Shandong, People's Republic of China
- Key Laboratory for Translational Oncolgoy, Xuzhou Medical University, Xuzhou, Jiangsu, People's Republic of China
| | - Shu Liu
- Central Laboratory, Linyi People's Hospital, Shandong University, Linyi, Shandong, People's Republic of China
- Department of Neurology, Linyi People's Hospital, Shandong University, Linyi, Shandong, People's Republic of China
- Key Laboratory of Neurophysiology, Health Commission of Shandong Province, Linyi, Shandong, People's Republic of China
- Key Laboratory of Neurophysiology, Linyi, Shandong, People's Republic of China
| | - Quanping Su
- Central Laboratory, Linyi People's Hospital, Shandong University, Linyi, Shandong, People's Republic of China
- Department of Neurology, Linyi People's Hospital, Shandong University, Linyi, Shandong, People's Republic of China
- Key Laboratory of Neurophysiology, Health Commission of Shandong Province, Linyi, Shandong, People's Republic of China
- Key Laboratory of Neurophysiology, Linyi, Shandong, People's Republic of China
| | - Fengyuan Che
- Central Laboratory, Linyi People's Hospital, Shandong University, Linyi, Shandong, People's Republic of China.
- Department of Neurology, Linyi People's Hospital, Shandong University, Linyi, Shandong, People's Republic of China.
- Key Laboratory of Neurophysiology, Health Commission of Shandong Province, Linyi, Shandong, People's Republic of China.
- Key Laboratory of Neurophysiology, Linyi, Shandong, People's Republic of China.
| | - Lijuan Wang
- Central Laboratory, Linyi People's Hospital, Shandong University, Linyi, Shandong, People's Republic of China.
- Key Laboratory of Tumor Biology, Linyi, Shandong, People's Republic of China.
- Key Laboratory for Translational Oncolgoy, Xuzhou Medical University, Xuzhou, Jiangsu, People's Republic of China.
- Department of Hematology, Linyi People's Hospital, Shandong University, Linyi, Shandong, People's Republic of China.
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16
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Kątnik E, Gomułkiewicz A, Piotrowska A, Grzegrzółka J, Rusak A, Kmiecik A, Ratajczak-Wielgomas K, Dzięgiel P. BCL11A Expression in Breast Cancer. Curr Issues Mol Biol 2023; 45:2681-2698. [PMID: 37185699 PMCID: PMC10137054 DOI: 10.3390/cimb45040175] [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: 02/16/2023] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 05/17/2023] Open
Abstract
B-cell leukemia/lymphoma 11A (BCL11A) is a transcription factor that regulates the expression of genes involved in cell division or apoptosis. A link between high BCL11A expression and a worse prognosis has been demonstrated in patients with various cancers. The aim of this study was to investigate the expression pattern of BCL11A in breast cancer (BC) cases and mastopathy samples and to correlate the results with the clinicopathological data. The expression of the BCL11A protein was investigated using immunohistochemistry (IHC) on 200 cases of BC and 13 mastopathy samples. The level of BCL11A mRNA was determined using real-time PCR in 22 cases of BC and 6 mastopathy samples. The expression of BCL11A was also examined at the protein and mRNA levels in BC cell lines. A higher expression level of BCL11A in BC cases was shown compared to mastopathy samples. The expression level of BCL11A in BC cases and in the studied cell lines decreased with the increasing grade of histological malignancy (G). It was also negatively correlated with the primary tumor size. A significantly lower expression of BCL11A was found in BC that did not express estrogen or progesterone receptors and in triple-negative cases. The results of our research suggest that BCL11A may be relevant in the development of BC.
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Affiliation(s)
- Ewa Kątnik
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland
| | - Agnieszka Gomułkiewicz
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland
| | - Aleksandra Piotrowska
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland
| | - Jędrzej Grzegrzółka
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland
| | - Agnieszka Rusak
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland
| | - Alicja Kmiecik
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland
| | - Katarzyna Ratajczak-Wielgomas
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland
| | - Piotr Dzięgiel
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland
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17
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Andrades A, Peinado P, Alvarez-Perez JC, Sanjuan-Hidalgo J, García DJ, Arenas AM, Matia-González AM, Medina PP. SWI/SNF complexes in hematological malignancies: biological implications and therapeutic opportunities. Mol Cancer 2023; 22:39. [PMID: 36810086 PMCID: PMC9942420 DOI: 10.1186/s12943-023-01736-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/30/2023] [Indexed: 02/23/2023] Open
Abstract
Hematological malignancies are a highly heterogeneous group of diseases with varied molecular and phenotypical characteristics. SWI/SNF (SWItch/Sucrose Non-Fermentable) chromatin remodeling complexes play significant roles in the regulation of gene expression, being essential for processes such as cell maintenance and differentiation in hematopoietic stem cells. Furthermore, alterations in SWI/SNF complex subunits, especially in ARID1A/1B/2, SMARCA2/4, and BCL7A, are highly recurrent across a wide variety of lymphoid and myeloid malignancies. Most genetic alterations cause a loss of function of the subunit, suggesting a tumor suppressor role. However, SWI/SNF subunits can also be required for tumor maintenance or even play an oncogenic role in certain disease contexts. The recurrent alterations of SWI/SNF subunits highlight not only the biological relevance of SWI/SNF complexes in hematological malignancies but also their clinical potential. In particular, increasing evidence has shown that mutations in SWI/SNF complex subunits confer resistance to several antineoplastic agents routinely used for the treatment of hematological malignancies. Furthermore, mutations in SWI/SNF subunits often create synthetic lethality relationships with other SWI/SNF or non-SWI/SNF proteins that could be exploited therapeutically. In conclusion, SWI/SNF complexes are recurrently altered in hematological malignancies and some SWI/SNF subunits may be essential for tumor maintenance. These alterations, as well as their synthetic lethal relationships with SWI/SNF and non-SWI/SNF proteins, may be pharmacologically exploited for the treatment of diverse hematological cancers.
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Affiliation(s)
- Alvaro Andrades
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Paola Peinado
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain ,grid.451388.30000 0004 1795 1830Present Address: The Francis Crick Institute, London, UK
| | - Juan Carlos Alvarez-Perez
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Juan Sanjuan-Hidalgo
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain
| | - Daniel J. García
- grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.4489.10000000121678994Department of Biochemistry and Molecular Biology III and Immunology, University of Granada, Granada, Spain
| | - Alberto M. Arenas
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Ana M. Matia-González
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Pedro P. Medina
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
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18
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Shin B, Rothenberg EV. Multi-modular structure of the gene regulatory network for specification and commitment of murine T cells. Front Immunol 2023; 14:1108368. [PMID: 36817475 PMCID: PMC9928580 DOI: 10.3389/fimmu.2023.1108368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 01/11/2023] [Indexed: 02/04/2023] Open
Abstract
T cells develop from multipotent progenitors by a gradual process dependent on intrathymic Notch signaling and coupled with extensive proliferation. The stages leading them to T-cell lineage commitment are well characterized by single-cell and bulk RNA analyses of sorted populations and by direct measurements of precursor-product relationships. This process depends not only on Notch signaling but also on multiple transcription factors, some associated with stemness and multipotency, some with alternative lineages, and others associated with T-cell fate. These factors interact in opposing or semi-independent T cell gene regulatory network (GRN) subcircuits that are increasingly well defined. A newly comprehensive picture of this network has emerged. Importantly, because key factors in the GRN can bind to markedly different genomic sites at one stage than they do at other stages, the genes they significantly regulate are also stage-specific. Global transcriptome analyses of perturbations have revealed an underlying modular structure to the T-cell commitment GRN, separating decisions to lose "stem-ness" from decisions to block alternative fates. Finally, the updated network sheds light on the intimate relationship between the T-cell program, which depends on the thymus, and the innate lymphoid cell (ILC) program, which does not.
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Affiliation(s)
- Boyoung Shin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Ellen V. Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
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19
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Decoding transcriptional regulation via a human gene expression predictor. J Genet Genomics 2023; 50:305-317. [PMID: 36693565 DOI: 10.1016/j.jgg.2023.01.006] [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: 09/02/2022] [Revised: 01/04/2023] [Accepted: 01/10/2023] [Indexed: 01/22/2023]
Abstract
Transcription factors (TFs) regulate cellular activities by controlling gene expression, but a predictive model describing how TFs quantitatively modulate human transcriptomes is lacking. We construct a universal human gene expression predictor and utilize it to decode transcriptional regulation. Using the expression of 1613 TFs, the predictor reconstitutes highly accurate transcriptomes for samples derived from a wide range of tissues and conditions. The broad applicability of the predictor indicates that it recapitulates the quantitative relationships between TFs and target genes ubiquitous across tissues. Significant interacting TF-target gene pairs are extracted from the predictor and enable downstream inference of TF regulators for diverse pathways involved in development, immunity, metabolism, and stress response. A detailed analysis of the hematopoiesis process reveals an atlas of key TFs regulating the development of different hematopoietic cell lineages, and a portion of these TFs are conserved between humans and mice. The results demonstrate that our method is capable of delineating the TFs responsible for fate determination. Compared to other existing tools, our approach shows better performance in recovering the correct TF regulators. Thus, we present a novel approach that can be used to study human transcriptional regulation in general.
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20
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Park SH, Cao M, Pan Y, Davis TH, Saxena L, Deshmukh H, Fu Y, Treangen T, Sheehan VA, Bao G. Comprehensive analysis and accurate quantification of unintended large gene modifications induced by CRISPR-Cas9 gene editing. SCIENCE ADVANCES 2022; 8:eabo7676. [PMID: 36269834 PMCID: PMC9586483 DOI: 10.1126/sciadv.abo7676] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 09/02/2022] [Indexed: 05/23/2023]
Abstract
Most genome editing analyses to date are based on quantifying small insertions and deletions. Here, we show that CRISPR-Cas9 genome editing can induce large gene modifications, such as deletions, insertions, and complex local rearrangements in different primary cells and cell lines. We analyzed large deletion events in hematopoietic stem and progenitor cells (HSPCs) using different methods, including clonal genotyping, droplet digital polymerase chain reaction, single-molecule real-time sequencing with unique molecular identifier, and long-amplicon sequencing assay. Our results show that large deletions of up to several thousand bases occur with high frequencies at the Cas9 on-target cut sites on the HBB (11.7 to 35.4%), HBG (14.3%), and BCL11A (13.2%) genes in HSPCs and the PD-1 (15.2%) gene in T cells. Our findings have important implications to advancing genome editing technologies for treating human diseases, because unintended large gene modifications may persist, thus altering the biological functions and reducing the available therapeutic alleles.
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Affiliation(s)
- So Hyun Park
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Mingming Cao
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Yidan Pan
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Timothy H. Davis
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Lavanya Saxena
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | | | - Yilei Fu
- Department of Computer Science, Rice University, Houston, TX 77005, USA
| | - Todd Treangen
- Department of Computer Science, Rice University, Houston, TX 77005, USA
| | | | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
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21
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Bone marrow-derived naïve B lymphocytes improve heart function after myocardial infarction: a novel cardioprotective mechanism for empagliflozin. Basic Res Cardiol 2022; 117:47. [PMID: 36171393 DOI: 10.1007/s00395-022-00956-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 09/01/2022] [Accepted: 09/20/2022] [Indexed: 01/31/2023]
Abstract
The role of adaptive immunity in myocardial recovery post myocardial infarction (MI), particularly the immune response by B lymphocytes, remains elusive. Bone marrow immune microenvironment in response to MI is remotely regulated by the hypothalamic pituitary adrenal (HPA) axis. We utilized the cardioprotective actions of SGLT2 inhibitor to identify and characterize bone marrow B cell subsets that respond to myocardial injury. Initially, we preformed ligation of left anterior descendant (LAD) coronary artery in male C57BL/6J mice to monitor the dynamic changes of immune cells across tissues. Mechanistic insights from mouse models demonstrated arrest of bone marrow B cell maturation and function 24 h post MI. A secondary MI model (twice MIs) in mice was established for the first time to evaluate the dosage-dependent cardioprotection of empagliflozin (EMPA). Single-cell RNA-Seq further demonstrated that EMPA restored bone marrow naïve B cell (B220+CD19+CD43-IgM+IgD+) counts and function. Additionally, we recruited 14 acute MI patients with single LAD disease, and profiled B cells post percutaneous coronary intervention (PCI) (compared to 18 matched no-MI controls). We revealed a positive correlation of increased B cell counts with enhanced ejection fraction in MI patients with PCI while lymphopenia was associated with patients with heart failure. Mechanistically, MI triggers the release of glucocorticoids from neuroendocrine system, inducing NHE1-mediated autophagic death of bone marrow B cells while repressing B cell progenitor proliferation and differentiation. Infusion of B cells derived from bone marrow significantly improved cardiac function and diminished infarct size post MI. These findings provide new mechanistic insights into regulation of adaptive immune response post MI, and support targeting bone marrow B cell development for improved ventricular remodeling and reduced heart failure after MI.
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22
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Vickridge E, Faraco CCF, Tehrani PS, Ramdzan ZM, Djerir B, Rahimian H, Leduy L, Maréchal A, Gingras AC, Nepveu A. The DNA repair function of BCL11A suppresses senescence and promotes continued proliferation of triple-negative breast cancer cells. NAR Cancer 2022; 4:zcac028. [PMID: 36186110 PMCID: PMC9516615 DOI: 10.1093/narcan/zcac028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 09/08/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
We identified the BCL11A protein in a proximity-dependent biotinylation screen performed with the DNA glycosylase NTHL1. In vitro, DNA repair assays demonstrate that both BCL11A and a small recombinant BCL11A160-520 protein that is devoid of DNA binding and transcription regulatory domains can stimulate the enzymatic activities of two base excision repair enzymes: NTHL1 and DNA Pol β. Increased DNA repair efficiency, in particular of the base excision repair pathway, is essential for many cancer cells to proliferate in the presence of elevated reactive oxygen species (ROS) produced by cancer-associated metabolic changes. BCL11A is highly expressed in triple-negative breast cancers (TNBC) where its knockdown was reported to reduce clonogenicity and cause tumour regression. We show that BCL11A knockdown in TNBC cells delays repair of oxidative DNA damage, increases the number of oxidized bases and abasic sites in genomic DNA, slows down proliferation and induces cellular senescence. These phenotypes are rescued by ectopic expression of the short BCL11A160-520 protein. We further show that the BCL11A160-520 protein accelerates the repair of oxidative DNA damage and cooperates with RAS in cell transformation assays, thereby enabling cells to avoid senescence and continue to proliferate in the presence of high ROS levels.
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Affiliation(s)
- Elise Vickridge
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Québec H3A 1A3, Canada
| | - Camila C F Faraco
- Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Québec H3A 1A3, Canada
| | - Payman S Tehrani
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Zubaidah M Ramdzan
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Québec H3A 1A3, Canada
| | - Billel Djerir
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada
| | - Hedyeh Rahimian
- Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Québec H3A 1A3, Canada
| | - Lam Leduy
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Québec H3A 1A3, Canada
| | - Alexandre Maréchal
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Alain Nepveu
- To whom correspondence should be addressed. Tel: +1 514 398 5839; Fax: +1 514 398 6769;
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23
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Fu B, Liao J, Chen S, Li W, Wang Q, Hu J, Yang F, Hsiao S, Jiang Y, Wang L, Chen F, Zhang Y, Wang X, Li D, Liu M, Wu Y. CRISPR-Cas9-mediated gene editing of the BCL11A enhancer for pediatric β 0/β 0 transfusion-dependent β-thalassemia. Nat Med 2022; 28:1573-1580. [PMID: 35922667 DOI: 10.1038/s41591-022-01906-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 06/17/2022] [Indexed: 11/09/2022]
Abstract
Gene editing to disrupt the GATA1-binding site at the +58 BCL11A erythroid enhancer could induce γ-globin expression, which is a promising therapeutic strategy to alleviate β-hemoglobinopathy caused by HBB gene mutation. In the present study, we report the preliminary results of an ongoing phase 1/2 trial (NCT04211480) evaluating safety and efficacy of gene editing therapy in children with blood transfusion-dependent β-thalassemia (TDT). We transplanted BCL11A enhancer-edited, autologous, hematopoietic stem and progenitor cells into two children, one carrying the β0/β0 genotype, classified as the most severe type of TDT. Primary endpoints included engraftment, overall survival and incidence of adverse events (AEs). Both patients were clinically well with multilineage engraftment, and all AEs to date were considered unrelated to gene editing and resolved after treatment. Secondary endpoints included achieving transfusion independence, editing rate in bone marrow cells and change in hemoglobin (Hb) concentration. Both patients achieved transfusion independence for >18 months after treatment, and their Hb increased from 8.2 and 10.8 g dl-1 at screening to 15.0 and 14.0 g dl-1 at the last visit, respectively, with 85.46% and 89.48% editing persistence in bone marrow cells. Exploratory analysis of single-cell transcriptome and indel patterns in edited peripheral blood mononuclear cells showed no notable side effects of the therapy.
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Affiliation(s)
- Bin Fu
- Xiangya Hospital, Central South University, Hunan, China.
| | - Jiaoyang Liao
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Shuanghong Chen
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Wei Li
- Bioray Laboratories Inc., Shanghai, China
| | - Qiudao Wang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jian Hu
- Xiangya Hospital, Central South University, Hunan, China
| | - Fei Yang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Shenlin Hsiao
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Yanhong Jiang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Liren Wang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Fangping Chen
- Xiangya Hospital, Central South University, Hunan, China
| | - Yuanjin Zhang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Xin Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Dali Li
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China. .,Bioray Laboratories Inc., Shanghai, China.
| | - Mingyao Liu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China. .,Bioray Laboratories Inc., Shanghai, China.
| | - Yuxuan Wu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.
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24
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Qu J, Yang F, Zhu T, Wang Y, Fang W, Ding Y, Zhao X, Qi X, Xie Q, Chen M, Xu Q, Xie Y, Sun Y, Chen D. A reference single-cell regulomic and transcriptomic map of cynomolgus monkeys. Nat Commun 2022; 13:4069. [PMID: 35831300 PMCID: PMC9279386 DOI: 10.1038/s41467-022-31770-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 07/01/2022] [Indexed: 12/24/2022] Open
Abstract
Non-human primates are attractive laboratory animal models that accurately reflect both developmental and pathological features of humans. Here we present a compendium of cell types across multiple organs in cynomolgus monkeys (Macaca fascicularis) using both single-cell chromatin accessibility and RNA sequencing data. The integrated cell map enables in-depth dissection and comparison of molecular dynamics, cell-type compositions and cellular heterogeneity across multiple tissues and organs. Using single-cell transcriptomic data, we infer pseudotime cell trajectories and cell-cell communications to uncover key molecular signatures underlying their cellular processes. Furthermore, we identify various cell-specific cis-regulatory elements and construct organ-specific gene regulatory networks at the single-cell level. Finally, we perform comparative analyses of single-cell landscapes among mouse, monkey and human. We show that cynomolgus monkey has strikingly higher degree of similarities in terms of immune-associated gene expression patterns and cellular communications to human than mouse. Taken together, our study provides a valuable resource for non-human primate cell biology. Non-human primates are attractive laboratory animal models that can accurately reflect some developmental and pathological features of humans. Here the authors chart a reference cell map of cynomolgus monkeys using both scATAC-seq and scRNA-seq data across multiple organs, providing insights into the molecular dynamics and cellular heterogeneity of this organism.
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Affiliation(s)
- Jiao Qu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China
| | - Fa Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China
| | - Tao Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China
| | - Yingshuo Wang
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 310052, Hangzhou, China
| | - Wen Fang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China
| | - Yan Ding
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China
| | - Xue Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China
| | - Xianjia Qi
- Shanghai XuRan Biotechnology Co., Ltd., 1088 Zhongchun Road, 201109, Shanghai, China
| | - Qiangmin Xie
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 310052, Hangzhou, China
| | - Ming Chen
- College of Life Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Qiang Xu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China
| | - Yicheng Xie
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 310052, Hangzhou, China.
| | - Yang Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China. .,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China.
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China.
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25
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Rahimmanesh I, Boshtam M, Kouhpayeh S, Khanahmad H, Dabiri A, Ahangarzadeh S, Esmaeili Y, Bidram E, Vaseghi G, Haghjooy Javanmard S, Shariati L, Zarrabi A, Varma RS. Gene Editing-Based Technologies for Beta-hemoglobinopathies Treatment. BIOLOGY 2022; 11:biology11060862. [PMID: 35741383 PMCID: PMC9219845 DOI: 10.3390/biology11060862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/19/2022] [Accepted: 05/31/2022] [Indexed: 06/12/2023]
Abstract
Beta (β)-thalassemia is a group of human inherited abnormalities caused by various molecular defects, which involves a decrease or cessation in the balanced synthesis of the β-globin chains in hemoglobin structure. Traditional treatment for β-thalassemia major is allogeneic bone marrow transplantation (BMT) from a completely matched donor. The limited number of human leukocyte antigen (HLA)-matched donors, long-term use of immunosuppressive regimen and higher risk of immunological complications have limited the application of this therapeutic approach. Furthermore, despite improvements in transfusion practices and chelation treatment, many lingering challenges have encouraged researchers to develop newer therapeutic strategies such as nanomedicine and gene editing. One of the most powerful arms of genetic manipulation is gene editing tools, including transcription activator-like effector nucleases, zinc-finger nucleases, and clustered regularly interspaced short palindromic repeat-Cas-associated nucleases. These tools have concentrated on γ- or β-globin addition, regulating the transcription factors involved in expression of endogenous γ-globin such as KLF1, silencing of γ-globin inhibitors including BCL11A, SOX6, and LRF/ZBTB7A, and gene repair strategies. In this review article, we present a systematic overview of the appliances of gene editing tools for β-thalassemia treatment and paving the way for patients' therapy.
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Affiliation(s)
- Ilnaz Rahimmanesh
- Applied Physiology Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan 73461-81746, Iran
| | - Maryam Boshtam
- Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan 81583-88994, Iran
| | - Shirin Kouhpayeh
- Erythron Genetics and Pathobiology Laboratory, Department of Immunology, Isfahan 76351-81647, Iran
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan 73461-81746, Iran
| | - Arezou Dabiri
- Applied Physiology Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan 73461-81746, Iran
| | - Shahrzad Ahangarzadeh
- Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan 73461-81746, Iran
| | - Yasaman Esmaeili
- Biosensor Research Center, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan 73461-81746, Iran
| | - Elham Bidram
- Biosensor Research Center, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan 73461-81746, Iran
- Department of Biomaterials, Nanotechnology and Tissue Engineering, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan 73461-81746, Iran
| | - Golnaz Vaseghi
- Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan 81583-88994, Iran
| | - Shaghayegh Haghjooy Javanmard
- Applied Physiology Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan 73461-81746, Iran
| | - Laleh Shariati
- Department of Biomaterials, Nanotechnology and Tissue Engineering, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan 73461-81746, Iran
- Cancer Prevention Research, Isfahan University of Medical Sciences, Isfahan 73461-81746, Iran
| | - Ali Zarrabi
- Department of Biomedical Engineering, Faculty of Engineering and Natural Sciences, Istinye University, Sariyer, Istanbul 34396, Turkey
| | - Rajender S Varma
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
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Down-regulation of the transcriptional repressor ZNF802 (JAZF1) reactivates fetal hemoglobin in β 0-thalassemia/HbE. Sci Rep 2022; 12:4952. [PMID: 35322124 PMCID: PMC8943019 DOI: 10.1038/s41598-022-08920-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 03/08/2022] [Indexed: 12/13/2022] Open
Abstract
Reactivating of fetal hemoglobin (HbF; α2γ2) can ameliorate the severity of β-thalassemia disease by compensating for adult hemoglobin deficiency in patients. Previously, microarray analysis revealed that zinc finger protein (ZNF)802 (also known as Juxta-posed with another zinc finger gene-1 (JAZF1)) was upregulated in human erythroblasts derived from adult peripheral blood compared with fetal liver-derived cells, implying a potential role as a HbF repressor. However, deficiency in ZNF802 induced by lentiviral shRNA in β0-thalassemia/hemoglobinE erythroblasts had no effect on erythroblast proliferation and differentiation. Remarkably, the induction of HBG expression was observed at the transcriptional and translational levels resulting in an increase of HbF to 35.0 ± 3.5%. Interestingly, the embryonic globin transcripts were also upregulated but the translation of embryonic globin was not detected. These results suggest ZNF802 might be a transcriptional repressor of the γ-globin gene in adult erythroid cells.
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Bhanja SK, Goel A, Mehra M, Bag S, Kharchec SD, Malakar D, Dash B. Microarray analysis and PCR validation of genes associated with facultative parthenogenesis in Meleagris gallopavo (Turkey). Theriogenology 2022; 186:86-94. [DOI: 10.1016/j.theriogenology.2022.03.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/10/2022] [Accepted: 03/27/2022] [Indexed: 10/18/2022]
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Thalor A, Kumar Joon H, Singh G, Roy S, Gupta D. Machine learning assisted analysis of breast cancer gene expression profiles reveals novel potential prognostic biomarkers for triple-negative breast cancer. Comput Struct Biotechnol J 2022; 20:1618-1631. [PMID: 35465161 PMCID: PMC9014315 DOI: 10.1016/j.csbj.2022.03.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/19/2022] [Accepted: 03/21/2022] [Indexed: 12/12/2022] Open
Abstract
Tumor heterogeneity and the unclear metastasis mechanisms are the leading cause for the unavailability of effective targeted therapy for Triple-negative breast cancer (TNBC), a breast cancer (BrCa) subtype characterized by high mortality and high frequency of distant metastasis cases. The identification of prognostic biomarker can improve prognosis and personalized treatment regimes. Herein, we collected gene expression datasets representing TNBC and Non-TNBC BrCa. From the complete dataset, a subset reflecting solely known cancer driver genes was also constructed. Recursive Feature Elimination (RFE) was employed to identify top 20, 25, 30, 35, 40, 45, and 50 gene signatures that differentiate TNBC from the other BrCa subtypes. Five machine learning algorithms were employed on these selected features and on the basis of model performance evaluation, it was found that for the complete and driver dataset, XGBoost performs the best for a subset of 25 and 20 genes, respectively. Out of these 45 genes from the two datasets, 34 genes were found to be differentially regulated. The Kaplan-Meier (KM) analysis for Distant Metastasis Free Survival (DMFS) of these 34 differentially regulated genes revealed four genes, out of which two are novel that could be potential prognostic genes (POU2AF1 and S100B). Finally, interactome and pathway enrichment analyses were carried out to investigate the functional role of the identified potential prognostic genes in TNBC. These genes are associated with MAPK, PI3-AkT, Wnt, TGF-β, and other signal transduction pathways, pivotal in metastasis cascade. These gene signatures can provide novel molecular-level insights into metastasis.
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Affiliation(s)
- Anamika Thalor
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Hemant Kumar Joon
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
- Regional Centre for Biotechnology, Faridabad 121001, Haryana, India
| | - Gagandeep Singh
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shikha Roy
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
- Corresponding author at: Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, India.
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Dalod M, Scheu S. Dendritic cell functions in vivo: a user's guide to current and next generation mutant mouse models. Eur J Immunol 2022; 52:1712-1749. [PMID: 35099816 DOI: 10.1002/eji.202149513] [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: 11/19/2021] [Accepted: 01/14/2022] [Indexed: 11/11/2022]
Abstract
Dendritic cells (DCs) do not just excel in antigen presentation. They orchestrate information transfer from innate to adaptive immunity, by sensing and integrating a variety of danger signals, and translating them to naïve T cells, to mount specifically tailored immune responses. This is accomplished by distinct DC types specialized in different functions and because each DC is functionally plastic, assuming different activation states depending on the input signals received. Mouse models hold the key to untangle this complexity and determine which DC types and activation states contribute to which functions. Here, we aim to provide comprehensive information for selecting the most appropriate mutant mouse strains to address specific research questions on DCs, considering three in vivo experimental approaches: (i) interrogating the roles of DC types through their depletion; (ii) determining the underlying mechanisms by specific genetic manipulations; (iii) deciphering the spatiotemporal dynamics of DC responses. We summarize the advantages, caveats, suggested use and perspectives for a variety of mutant mouse strains, discussing in more detail the most widely used or accurate models. Finally, we discuss innovative strategies to improve targeting specificity, for the next generation mutant mouse models, and briefly address how humanized mouse models can accelerate translation into the clinic. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Marc Dalod
- CNRS, Inserm, Aix Marseille Univ, Centre d'Immunologie de Marseille-Luminy (CIML), Turing Center for Living Systems, Marseille, France
| | - Stefanie Scheu
- Institute of Medical Microbiology and Hospital Hygiene, University of Düsseldorf, Düsseldorf, Germany
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Papasavva PL, Patsali P, Loucari CC, Kurita R, Nakamura Y, Kleanthous M, Lederer CW. CRISPR Editing Enables Consequential Tag-Activated MicroRNA-Mediated Endogene Deactivation. Int J Mol Sci 2022; 23:1082. [PMID: 35163006 PMCID: PMC8834719 DOI: 10.3390/ijms23031082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/09/2022] [Accepted: 01/12/2022] [Indexed: 02/01/2023] Open
Abstract
Molecular therapies and functional studies greatly benefit from spatial and temporal precision of genetic intervention. We therefore conceived and explored tag-activated microRNA (miRNA)-mediated endogene deactivation (TAMED) as a research tool and potential lineage-specific therapy. For proof of principle, we aimed to deactivate γ-globin repressor BCL11A in erythroid cells by tagging the 3' untranslated region (UTR) of BCL11A with miRNA recognition sites (MRSs) for the abundant erythromiR miR-451a. To this end, we employed nucleofection of CRISPR/Cas9 ribonucleoprotein (RNP) particles alongside double- or single-stranded oligodeoxynucleotides for, respectively, non-homologous-end-joining (NHEJ)- or homology-directed-repair (HDR)-mediated MRS insertion. NHEJ-based tagging was imprecise and inefficient (≤6%) and uniformly produced knock-in- and indel-containing MRS tags, whereas HDR-based tagging was more efficient (≤18%), but toxic for longer donors encoding concatenated and thus potentially more efficient MRS tags. Isolation of clones for robust HEK293T cells tagged with a homozygous quadruple MRS resulted in 25% spontaneous reduction in BCL11A and up to 36% reduction after transfection with an miR-451a mimic. Isolation of clones for human umbilical cord blood-derived erythroid progenitor-2 (HUDEP-2) cells tagged with single or double MRS allowed detection of albeit weak γ-globin induction. Our study demonstrates suitability of TAMED for physiologically relevant modulation of gene expression and its unsuitability for therapeutic application in its current form.
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Affiliation(s)
- Panayiota L. Papasavva
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (P.L.P.); (P.P.); (C.C.L.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
| | - Petros Patsali
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (P.L.P.); (P.P.); (C.C.L.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
| | - Constantinos C. Loucari
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (P.L.P.); (P.P.); (C.C.L.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
| | - Ryo Kurita
- Research and Development Department, Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, Koto-ku, Tokyo 135-8521, Japan;
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research Center, Tsukuba 305-0074, Japan;
| | - Marina Kleanthous
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (P.L.P.); (P.P.); (C.C.L.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
| | - Carsten W. Lederer
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (P.L.P.); (P.P.); (C.C.L.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
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31
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Demirci S, Leonard A, Essawi K, Tisdale JF. CRISPR-Cas9 to induce fetal hemoglobin for the treatment of sickle cell disease. Mol Ther Methods Clin Dev 2021; 23:276-285. [PMID: 34729375 PMCID: PMC8526756 DOI: 10.1016/j.omtm.2021.09.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Genome editing is potentially a curative technique available to all individuals with β-hemoglobinopathies, including sickle cell disease (SCD). Fetal hemoglobin (HbF) inhibits sickle hemoglobin (HbS) polymerization, and it is well described that naturally occurring hereditary persistence of HbF (HPFH) alleviates disease symptoms; therefore, reawakening of developmentally silenced HbF in adult red blood cells (RBCs) has long been of interest as a therapeutic strategy. Recent advances in genome editing platforms, particularly with the use of CRISPR-Cas9, have paved the way for efficient HbF induction through the creation of artificial HPFH mutations, editing of transcriptional HbF silencers, and modulating epigenetic intermediates that govern HbF expression. Clinical trials investigating BCL11A enhancer editing in patients with β-hemoglobinopathies have demonstrated promising results, although follow-up is short and the number of patients treated to date is low. While practical, economic, and clinical challenges of genome editing are well recognized by the scientific community, potential solutions to overcome these hurdles are in development. Here, we review the recent progress and obstacles yet to be overcome for the most effective and feasible HbF reactivation practice using CRISPR-Cas9 genome editing as a curative strategy for patients with SCD.
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Affiliation(s)
- Selami Demirci
- Cellular and Molecular Therapeutics Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20814, USA
| | - Alexis Leonard
- Cellular and Molecular Therapeutics Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20814, USA
| | - Khaled Essawi
- Cellular and Molecular Therapeutics Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20814, USA
- Department of Medical Laboratory Science, College of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - John F. Tisdale
- Cellular and Molecular Therapeutics Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20814, USA
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32
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Genome editing in large animal models. Mol Ther 2021; 29:3140-3152. [PMID: 34601132 DOI: 10.1016/j.ymthe.2021.09.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/26/2021] [Accepted: 09/26/2021] [Indexed: 12/21/2022] Open
Abstract
Although genome editing technologies have the potential to revolutionize the way we treat human diseases, barriers to successful clinical implementation remain. Increasingly, preclinical large animal models are being used to overcome these barriers. In particular, the immunogenicity and long-term safety of novel gene editing therapeutics must be evaluated rigorously. However, short-lived small animal models, such as mice and rats, cannot address secondary pathologies that may arise years after a gene editing treatment. Likewise, immunodeficient mouse models by definition lack the ability to quantify the host immune response to a novel transgene or gene-edited locus. Large animal models, including dogs, pigs, and non-human primates (NHPs), bear greater resemblance to human anatomy, immunology, and lifespan and can be studied over longer timescales with clinical dosing regimens that are more relevant to humans. These models allow for larger scale and repeated blood and tissue sampling, enabling greater depth of study and focus on rare cellular subsets. Here, we review current progress in the development and evaluation of novel genome editing therapies in large animal models, focusing on applications in human immunodeficiency virus 1 (HIV-1) infection, cancer, and genetic diseases including hemoglobinopathies, Duchenne muscular dystrophy (DMD), hypercholesterolemia, and inherited retinal diseases.
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BCL11A promotes myeloid leukemogenesis by repressing PU.1 target genes. Blood Adv 2021; 6:1827-1843. [PMID: 34714913 PMCID: PMC8941473 DOI: 10.1182/bloodadvances.2021004558] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 10/04/2021] [Indexed: 11/20/2022] Open
Abstract
BCL11A promotes myeloid leukemogenesis via the repression of PU.1 target genes. Inhibition of corepressors abrogates the BCL11A function, inducing growth suppression and inhibition of engraftment in AML.
The transcriptional repressor BCL11A is involved in hematological malignancies, B-cell development, and fetal-to-adult hemoglobin switching. However, the molecular mechanism by which it promotes the development of myeloid leukemia remains largely unknown. We find that Bcl11a cooperates with the pseudokinase Trib1 in the development of acute myeloid leukemia (AML). Bcl11a promotes the proliferation and engraftment of Trib1-expressing AML cells in vitro and in vivo. Chromatin immunoprecipitation sequencing analysis showed that, upon DNA binding, Bcl11a is significantly associated with PU.1, an inducer of myeloid differentiation, and that Bcl11a represses several PU.1 target genes, such as Asb2, Clec5a, and Fcgr3. Asb2, as a Bcl11a target gene that modulates cytoskeleton and cell-cell interaction, plays a key role in Bcl11a-induced malignant progression. The repression of PU.1 target genes by Bcl11a is achieved by sequence-specific DNA-binding activity and recruitment of corepressors by Bcl11a. Suppression of the corepressor components HDAC and LSD1 reverses the repressive activity. Moreover, treatment of AML cells with the HDAC inhibitor pracinostat and the LSD1 inhibitor GSK2879552 resulted in growth inhibition in vitro and in vivo. High BCL11A expression is associated with worse prognosis in humans with AML. Blocking of BCL11A expression upregulates the expression of PU.1 target genes and inhibits the growth of HL-60 cells and their engraftment to the bone marrow, suggesting that BCL11A is involved in human myeloid malignancies via the suppression of PU.1 transcriptional activity.
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34
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Psatha N, Georgakopoulou A, Li C, Nandakumar V, Georgolopoulos G, Acosta R, Paschoudi K, Nelson J, Chee D, Athanasiadou A, Kouvatsi A, Funnell APW, Lieber A, Yannaki E, Papayannopoulou T. Enhanced HbF reactivation by multiplex mutagenesis of thalassemic CD34+ cells in vitro and in vivo. Blood 2021; 138:1540-1553. [PMID: 34086867 PMCID: PMC8554647 DOI: 10.1182/blood.2020010020] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 05/27/2021] [Indexed: 11/20/2022] Open
Abstract
Thalassemia or sickle cell patients with hereditary persistence of fetal hemoglobin (HbF) have an ameliorated clinical phenotype and, in some cases, can achieve transfusion independence. Inactivation via genome editing of γ-globin developmental suppressors, such as BCL11A or LRF/ZBTB7A, or of their binding sites, have been shown to significantly increase expression of endogenous HbF. To broaden the therapeutic window beyond a single-editing approach, we have explored combinations of cis- and trans-editing targets to enhance HbF reactivation. Multiplex mutagenesis in adult CD34+ cells was well tolerated and did not lead to any detectable defect in the cells' proliferation and differentiation, either in vitro or in vivo. The combination of 1 trans and 1 cis mutation resulted in high editing retention in vivo, coupled with almost pancellular HbF expression in NBSGW mice. The greater in vivo performance of this combination was also recapitulated using a novel helper-dependent adenoviral-CRISPR vector (HD-Ad-dualCRISPR) in CD34+ cells from β-thalassemia patients transplanted to NBSGW mice. A pronounced increase in HbF expression was observed in human red blood cells in mice with established predominant β0/β0-thalassemic hemopoiesis after in vivo injection of the HD-Ad-dualCRISPR vector. Collectively, our data suggest that the combination of cis and trans fetal globin reactivation mutations has the potential to significantly increase HbF both totally and on a per cell basis over single editing and could thus provide significant clinical benefit to patients with severe β-globin phenotype.
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Affiliation(s)
| | - Aphrodite Georgakopoulou
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Gene and Cell Therapy Center, Hematology Department-Hematopoietic Cell Transplantation Unit, George Papanikolaou Hospital, Thessaloniki, Greece; and
| | - Chang Li
- Division of Medical Genetics and
| | | | | | - Reyes Acosta
- Altius Institute for Biomedical Sciences, Seattle, WA
| | - Kiriaki Paschoudi
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Gene and Cell Therapy Center, Hematology Department-Hematopoietic Cell Transplantation Unit, George Papanikolaou Hospital, Thessaloniki, Greece; and
| | - Jemma Nelson
- Altius Institute for Biomedical Sciences, Seattle, WA
| | - Daniel Chee
- Altius Institute for Biomedical Sciences, Seattle, WA
| | - Anastasia Athanasiadou
- Gene and Cell Therapy Center, Hematology Department-Hematopoietic Cell Transplantation Unit, George Papanikolaou Hospital, Thessaloniki, Greece; and
| | - Anastasia Kouvatsi
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | | | - Evangelia Yannaki
- Gene and Cell Therapy Center, Hematology Department-Hematopoietic Cell Transplantation Unit, George Papanikolaou Hospital, Thessaloniki, Greece; and
- Division of Hematology, University of Washington, Seattle, WA
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35
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Demirci S, Leonard A, Tisdale JF. Genome editing strategies for fetal hemoglobin induction in beta-hemoglobinopathies. Hum Mol Genet 2021; 29:R100-R106. [PMID: 32406490 DOI: 10.1093/hmg/ddaa088] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 04/28/2020] [Accepted: 05/11/2020] [Indexed: 12/26/2022] Open
Abstract
Genome editing to correct a defective β-globin gene or induce fetal globin (HbF) for patients with beta-hemoglobinopathies has the potential to be a curative strategy available to all. HbF reactivation has long been an area of intense interest given the HbF inhibition of sickle hemoglobin (HbS) polymerization. Patients with HbS who also have high HbF tend to have less severe or even minimal clinical manifestations. Approaches to genetically engineer high HbF include de novo generation of naturally occurring hereditary persistence of fetal hemoglobin (HPFH) mutations, editing of transcriptional HbF repressors or their binding sites and/or regulating epigenetic intermediates controlling HbF expression. Recent preclinical and early clinical trial data show encouraging results; however, long-term follow-up is lacking, and the safety and efficacy concerns of genome editing remain.
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Affiliation(s)
- Selami Demirci
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes, National Institutes of Health, Bethesda, MD, USA
| | - Alexis Leonard
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes, National Institutes of Health, Bethesda, MD, USA
| | - John F Tisdale
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes, National Institutes of Health, Bethesda, MD, USA
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36
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Sun J, Wang J, Zheng D, Hu X. Advances in therapeutic application of CRISPR-Cas9. Brief Funct Genomics 2021; 19:164-174. [PMID: 31769791 DOI: 10.1093/bfgp/elz031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/04/2019] [Accepted: 10/03/2019] [Indexed: 02/06/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) is one of the most versatile and efficient gene editing technologies, which is derived from adaptive immune strategies for bacteria and archaea. With the remarkable development of programmable nuclease-based genome engineering these years, CRISPR-Cas9 system has developed quickly in recent 5 years and has been widely applied in countless areas, including genome editing, gene function investigation and gene therapy both in vitro and in vivo. In this paper, we briefly introduce the mechanisms of CRISPR-Cas9 tool in genome editing. More importantly, we review the recent therapeutic application of CRISPR-Cas9 in various diseases, including hematologic diseases, infectious diseases and malignant tumor. Finally, we discuss the current challenges and consider thoughtfully what advances are required in order to further develop the therapeutic application of CRISPR-Cas9 in the future.
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Affiliation(s)
- Jinyu Sun
- Sparkfire Scientific Research Group, Nanjing Medical University, China
| | - Jianchu Wang
- Department of Hepatobiliary Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, No. 18 Zhongshan Road, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Donghui Zheng
- Department of Nephrology, Huai'an Second People's Hospital and The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China
| | - Xiaorong Hu
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
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37
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Lee SR, Qian M, Yang W, Diedrich JD, Raetz E, Yang W, Dong Q, Devidas M, Pei D, Yeoh A, Cheng C, Pui CH, Evans WE, Mullighan CG, Hunger SP, Savic D, Relling MV, Loh ML, Yang JJ. Genome-Wide Association Study of Susceptibility Loci for TCF3-PBX1 Acute Lymphoblastic Leukemia in Children. J Natl Cancer Inst 2021; 113:933-937. [PMID: 32882024 PMCID: PMC8487647 DOI: 10.1093/jnci/djaa133] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/14/2020] [Accepted: 08/20/2020] [Indexed: 01/03/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common cancer in children. TCF3-PBX1 fusion defines a common molecular subtype of ALL with unique clinical features, but the molecular basis of its inherited susceptibility is unknown. In a genome-wide association study of 1494 ALL cases and 2057 non-ALL controls, we identified a germline risk locus located in an intergenic region between BCL11A and PAPOLG: rs2665658, P = 1.88 × 10-8 for TCF3-PBX1 ALL vs non-ALL, and P = 1.70 × 10-8 for TCF3-PBX1 ALL vs other-ALL. The lead variant was validated in a replication cohort, and conditional analyses pointed to a single causal variant with subtype-specific effect. The risk variant is located in a regulatory DNA element uniquely activated in ALL cells with the TCF3-PBX1 fusion and may distally modulate the transcription of the adjacent gene REL. Our results expand the understanding of subtype-specific ALL susceptibility and highlight plausible interplay between germline variants and somatic genomic abnormalities in ALL pathogenesis.
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Affiliation(s)
- Shawn H. R Lee
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
- Khoo Teck Puat–National University Children’s Medical Institute, National University Health System, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Maoxiang Qian
- Institute of Pediatrics and Department of Hematology and Oncology, Children’s Hospital of Fudan University, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Wentao Yang
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jonathan D Diedrich
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Elizabeth Raetz
- Division of Pediatric Hematology and Oncology, New York University Langone Health, New York, NY, USA
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Qian Dong
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Meenakshi Devidas
- Department of Global Pediatric Medicine, St Jude Children’s Research Hospital, Memphis, TN, USA
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - Deqing Pei
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Allen Yeoh
- Khoo Teck Puat–National University Children’s Medical Institute, National University Health System, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - William E Evans
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Stephen P Hunger
- Department of Pediatrics and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia and the Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel Savic
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children’s Hospital and the Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
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Salinas Cisneros G, Thein SL. Research in Sickle Cell Disease: From Bedside to Bench to Bedside. Hemasphere 2021; 5:e584. [PMID: 34095767 PMCID: PMC8171370 DOI: 10.1097/hs9.0000000000000584] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 04/17/2021] [Indexed: 01/25/2023] Open
Abstract
Sickle cell disease (SCD) is an exemplar of bidirectional translational research, starting with a remarkable astute observation of the abnormally shaped red blood cells that motivated decades of bench research that have now translated into new drugs and genetic therapies. Introduction of hydroxyurea (HU) therapy, the only SCD-modifying treatment for >30 years and now standard care, was initiated through another clinical observation by a pediatrician. While the clinical efficacy of HU is primarily due to its fetal hemoglobin (HbF) induction, the exact mechanism of how it increases HbF remains not fully understood. Unraveling of the molecular mechanism of how HU increases HbF has provided insights on the development of new HbF-reactivating agents in the pipeline. HU has other salutary effects, reduction of cellular adhesion to the vascular endothelium and inflammation, and dissecting these mechanisms has informed bench-both cellular and animal-research for development of the 3 recently approved agents: endari, voxelotor, and crizanlizumab; truly, a bidirectional bench to bedside translation. Decades of research to understand the mechanisms of fetal to adult hemoglobin have also culminated in promising anti-sickling genetic therapies and the first-in-human studies of reactivating an endogenous (γ-globin) gene HBG utilizing innovative genomic approaches.
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Affiliation(s)
- Gabriel Salinas Cisneros
- Sickle Cell Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
- Division of Hematology and Oncology, Children’s National Medical Center, Washington, District of Columbia, USA
| | - Swee Lay Thein
- Sickle Cell Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
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Wessels MW, Cnossen MH, van Dijk TB, Gillemans N, Schmidt KLJ, van Lom K, Vinjamur DS, Coyne S, Kurita R, Nakamura Y, de Man SA, Pfundt R, Azmani Z, Brouwer RWW, Bauer DE, van den Hout MCGN, van IJcken WFJ, Philipsen S. Molecular analysis of the erythroid phenotype of a patient with BCL11A haploinsufficiency. Blood Adv 2021; 5:2339-2349. [PMID: 33938942 PMCID: PMC8114548 DOI: 10.1182/bloodadvances.2020003753] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 03/12/2021] [Indexed: 12/29/2022] Open
Abstract
The BCL11A gene encodes a transcriptional repressor with essential functions in multiple tissues during human development. Haploinsufficiency for BCL11A causes Dias-Logan syndrome (OMIM 617101), an intellectual developmental disorder with hereditary persistence of fetal hemoglobin (HPFH). Due to the severe phenotype, disease-causing variants in BCL11A occur de novo. We describe a patient with a de novo heterozygous variant, c.1453G>T, in the BCL11A gene, resulting in truncation of the BCL11A-XL protein (p.Glu485X). The truncated protein lacks the 3 C-terminal DNA-binding zinc fingers and the nuclear localization signal, rendering it inactive. The patient displayed high fetal hemoglobin (HbF) levels (12.1-18.7% of total hemoglobin), in contrast to the parents who had HbF levels of 0.3%. We used cultures of patient-derived erythroid progenitors to determine changes in gene expression and chromatin accessibility. In addition, we investigated DNA methylation of the promoters of the γ-globin genes HBG1 and HBG2. HUDEP1 and HUDEP2 cells were used as models for fetal and adult human erythropoiesis, respectively. Similar to HUDEP1 cells, the patient's cells displayed Assay for Transposase-Accessible Chromatin (ATAC) peaks at the HBG1/2 promoters and significant expression of HBG1/2 genes. In contrast, HBG1/2 promoter methylation and genome-wide gene expression profiling were consistent with normal adult erythropoiesis. We conclude that HPFH is the major erythroid phenotype of constitutive BCL11A haploinsufficiency. Given the essential functions of BCL11A in other hematopoietic lineages and the neuronal system, erythroid-specific targeting of the BCL11A gene has been proposed for reactivation of γ-globin expression in β-hemoglobinopathy patients. Our data strongly support this approach.
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Affiliation(s)
| | - Marjon H Cnossen
- Department of Pediatric Hematology
- Academic Center for Hemoglobinopathies and Rare Anemias
| | - Thamar B van Dijk
- Academic Center for Hemoglobinopathies and Rare Anemias
- Department of Cell Biology, and
| | - Nynke Gillemans
- Academic Center for Hemoglobinopathies and Rare Anemias
- Department of Cell Biology, and
| | - K L Juliëtte Schmidt
- Academic Center for Hemoglobinopathies and Rare Anemias
- Department of Cell Biology, and
| | - Kirsten van Lom
- Academic Center for Hemoglobinopathies and Rare Anemias
- Department of Hematology, Erasmus MC, Rotterdam, The Netherlands
| | - Divya S Vinjamur
- Division of Hematology/Oncology, Department of Pediatric Oncology, Boston Children's Hospital, Boston, MA
- Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Boston, MA
- Broad Institute, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Steven Coyne
- Division of Hematology/Oncology, Department of Pediatric Oncology, Boston Children's Hospital, Boston, MA
- Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Boston, MA
- Broad Institute, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Ryo Kurita
- Department of Research and Development, Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN, BioResource Center, Tsukuba, Japan
| | - Stella A de Man
- Department of Pediatrics, Amphia Hospital, Breda, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; and
| | - Zakia Azmani
- Department of Cell Biology, and
- Center for Biomics, Erasmus MC, Rotterdam, The Netherlands
| | - Rutger W W Brouwer
- Department of Cell Biology, and
- Center for Biomics, Erasmus MC, Rotterdam, The Netherlands
| | - Daniel E Bauer
- Division of Hematology/Oncology, Department of Pediatric Oncology, Boston Children's Hospital, Boston, MA
- Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Boston, MA
- Broad Institute, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | | | - Wilfred F J van IJcken
- Department of Cell Biology, and
- Center for Biomics, Erasmus MC, Rotterdam, The Netherlands
| | - Sjaak Philipsen
- Academic Center for Hemoglobinopathies and Rare Anemias
- Department of Cell Biology, and
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ZNF410 represses fetal globin by singular control of CHD4. Nat Genet 2021; 53:719-728. [PMID: 33859416 PMCID: PMC8180380 DOI: 10.1038/s41588-021-00843-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/10/2021] [Indexed: 02/02/2023]
Abstract
Known fetal hemoglobin (HbF) silencers have potential on-target liabilities for rational β-hemoglobinopathy therapeutic inhibition. Here, through transcription factor (TF) CRISPR screening, we identify zinc-finger protein (ZNF) 410 as an HbF repressor. ZNF410 does not bind directly to the genes encoding γ-globins, but rather its chromatin occupancy is concentrated solely at CHD4, encoding the NuRD nucleosome remodeler, which is itself required for HbF repression. CHD4 has two ZNF410-bound regulatory elements with 27 combined ZNF410 binding motifs constituting unparalleled genomic clusters. These elements completely account for the effects of ZNF410 on fetal globin repression. Knockout of ZNF410 or its mouse homolog Zfp410 reduces CHD4 levels by 60%, enough to substantially de-repress HbF while eluding cellular or organismal toxicity. These studies suggest a potential target for HbF induction for β-hemoglobin disorders with a wide therapeutic index. More broadly, ZNF410 represents a special class of gene regulator, a conserved TF with singular devotion to regulation of a chromatin subcomplex.
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Sidwell T, Rothenberg EV. Epigenetic Dynamics in the Function of T-Lineage Regulatory Factor Bcl11b. Front Immunol 2021; 12:669498. [PMID: 33936112 PMCID: PMC8079813 DOI: 10.3389/fimmu.2021.669498] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/23/2021] [Indexed: 11/18/2022] Open
Abstract
The transcription factor Bcl11b is critically required to support the development of diverse cell types, including T lymphocytes, type 2 innate lymphoid cells, neurons, craniofacial mesenchyme and keratinocytes. Although in T cell development its onset of expression is tightly linked to T-lymphoid lineage commitment, the Bcl11b protein in fact regulates substantially different sets of genes in different lymphocyte populations, playing strongly context-dependent roles. Somewhat unusually for lineage-defining transcription factors with site-specific DNA binding activity, much of the reported chromatin binding of Bcl11b appears to be indirect, or guided in large part by interactions with other transcription factors. We describe evidence suggesting that a further way in which Bcl11b exerts such distinct stage-dependent functions is by nucleating changes in regional suites of epigenetic modifications through recruitment of multiple families of chromatin-modifying enzyme complexes. Herein we explore what is - and what remains to be - understood of the roles of Bcl11b, its cofactors, and how it modifies the epigenetic state of the cell to enforce its diverse set of context-specific transcriptional and developmental programs.
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Affiliation(s)
- Tom Sidwell
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Ellen V Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, United States
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Barbarani G, Labedz A, Stucchi S, Abbiati A, Ronchi AE. Physiological and Aberrant γ-Globin Transcription During Development. Front Cell Dev Biol 2021; 9:640060. [PMID: 33869190 PMCID: PMC8047207 DOI: 10.3389/fcell.2021.640060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/23/2021] [Indexed: 12/24/2022] Open
Abstract
The expression of the fetal Gγ- and Aγ-globin genes in normal development is confined to the fetal period, where two γ-globin chains assemble with two α-globin chains to form α2γ2 tetramers (HbF). HbF sustains oxygen delivery to tissues until birth, when β-globin replaces γ-globin, leading to the formation of α2β2 tetramers (HbA). However, in different benign and pathological conditions, HbF is expressed in adult cells, as it happens in the hereditary persistence of fetal hemoglobin, in anemias and in some leukemias. The molecular basis of γ-globin differential expression in the fetus and of its inappropriate activation in adult cells is largely unknown, although in recent years, a few transcription factors involved in this process have been identified. The recent discovery that fetal cells can persist to adulthood and contribute to disease raises the possibility that postnatal γ-globin expression could, in some cases, represent the signature of the fetal cellular origin.
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Affiliation(s)
- Gloria Barbarani
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
| | - Agata Labedz
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
| | - Sarah Stucchi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
| | - Alessia Abbiati
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
| | - Antonella E Ronchi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
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Insight of fetal to adult hemoglobin switch: Genetic modulators and therapeutic targets. Blood Rev 2021; 49:100823. [PMID: 33726930 DOI: 10.1016/j.blre.2021.100823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 02/08/2021] [Accepted: 03/03/2021] [Indexed: 01/31/2023]
Abstract
The clinical heterogeneity of β-hemoglobinopathies is so variable that it prompted the researchers to identify the genetic modulators of these diseases. Though the primary modulator is the type of β-globin mutation which affects the degree of β-globin chain synthesis, the co-inheritance of α-thalassemia and the fetal hemoglobin (HbF) levels also act as potent secondary genetic modifiers. As elevated HbF levels ameliorate the severity of hemoglobinopathies, in this review, the genetic modulators lying within and outside the β-globin gene cluster with their plausible role in governing the HbF levels have been summarised, which in future may act as potential therapeutic targets.
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Zittersteijn HA, Harteveld CL, Klaver-Flores S, Lankester AC, Hoeben RC, Staal FJT, Gonçalves MAFV. A Small Key for a Heavy Door: Genetic Therapies for the Treatment of Hemoglobinopathies. Front Genome Ed 2021; 2:617780. [PMID: 34713239 PMCID: PMC8525365 DOI: 10.3389/fgeed.2020.617780] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/14/2020] [Indexed: 12/26/2022] Open
Abstract
Throughout the past decades, the search for a treatment for severe hemoglobinopathies has gained increased interest within the scientific community. The discovery that ɤ-globin expression from intact HBG alleles complements defective HBB alleles underlying β-thalassemia and sickle cell disease, has provided a promising opening for research directed at relieving ɤ-globin repression mechanisms and, thereby, improve clinical outcomes for patients. Various gene editing strategies aim to reverse the fetal-to-adult hemoglobin switch to up-regulate ɤ-globin expression through disabling either HBG repressor genes or repressor binding sites in the HBG promoter regions. In addition to these HBB mutation-independent strategies involving fetal hemoglobin (HbF) synthesis de-repression, the expanding genome editing toolkit is providing increased accuracy to HBB mutation-specific strategies encompassing adult hemoglobin (HbA) restoration for a personalized treatment of hemoglobinopathies. Moreover, besides genome editing, more conventional gene addition strategies continue under investigation to restore HbA expression. Together, this research makes hemoglobinopathies a fertile ground for testing various innovative genetic therapies with high translational potential. Indeed, the progressive understanding of the molecular clockwork underlying the hemoglobin switch together with the ongoing optimization of genome editing tools heightens the prospect for the development of effective and safe treatments for hemoglobinopathies. In this context, clinical genetics plays an equally crucial role by shedding light on the complexity of the disease and the role of ameliorating genetic modifiers. Here, we cover the most recent insights on the molecular mechanisms underlying hemoglobin biology and hemoglobinopathies while providing an overview of state-of-the-art gene editing platforms. Additionally, current genetic therapies under development, are equally discussed.
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Affiliation(s)
- Hidde A. Zittersteijn
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Cornelis L. Harteveld
- Department of Human and Clinical Genetics, The Hemoglobinopathies Laboratory, Leiden University Medical Center, Leiden, Netherlands
| | | | - Arjan C. Lankester
- Department of Pediatrics, Stem Cell Transplantation Program, Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, Netherlands
| | - Rob C. Hoeben
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Frank J. T. Staal
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
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Frati G, Miccio A. Genome Editing for β-Hemoglobinopathies: Advances and Challenges. J Clin Med 2021; 10:482. [PMID: 33525591 PMCID: PMC7865242 DOI: 10.3390/jcm10030482] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/19/2021] [Accepted: 01/25/2021] [Indexed: 02/08/2023] Open
Abstract
β-hemoglobinopathies are the most common genetic disorders worldwide and are caused by mutations affecting the production or the structure of adult hemoglobin. Patients affected by these diseases suffer from anemia, impaired oxygen delivery to tissues, and multi-organ damage. In the absence of a compatible donor for allogeneic bone marrow transplantation, the lifelong therapeutic options are symptomatic care, red blood cell transfusions and pharmacological treatments. The last decades of research established lentiviral-mediated gene therapy as an efficacious therapeutic strategy. However, this approach is highly expensive and associated with a variable outcome depending on the effectiveness of the viral vector and the quality of the cell product. In the last years, genome editing emerged as a valuable tool for the development of curative strategies for β-hemoglobinopathies. Moreover, due to the wide range of its applications, genome editing has been extensively used to study regulatory mechanisms underlying globin gene regulation allowing the identification of novel genetic and pharmacological targets. In this work, we review the current advances and challenges of genome editing approaches to β-hemoglobinopathies. Special focus has been directed towards strategies aimed at correcting the defective β-globin gene or at inducing fetal hemoglobin (HbF), which are in an advanced state of clinical development.
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Affiliation(s)
- Giacomo Frati
- Laboratory of Chromatin and Gene Regulation during Development, Imagine Institute, Université de Paris, INSERM UMR 1163, F-75015 Paris, France
| | - Annarita Miccio
- Laboratory of Chromatin and Gene Regulation during Development, Imagine Institute, Université de Paris, INSERM UMR 1163, F-75015 Paris, France
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47
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Esrick EB, Lehmann LE, Biffi A, Achebe M, Brendel C, Ciuculescu MF, Daley H, MacKinnon B, Morris E, Federico A, Abriss D, Boardman K, Khelladi R, Shaw K, Negre H, Negre O, Nikiforow S, Ritz J, Pai SY, London WB, Dansereau C, Heeney MM, Armant M, Manis JP, Williams DA. Post-Transcriptional Genetic Silencing of BCL11A to Treat Sickle Cell Disease. N Engl J Med 2021; 384:205-215. [PMID: 33283990 PMCID: PMC7962145 DOI: 10.1056/nejmoa2029392] [Citation(s) in RCA: 221] [Impact Index Per Article: 73.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Sickle cell disease is characterized by hemolytic anemia, pain, and progressive organ damage. A high level of erythrocyte fetal hemoglobin (HbF) comprising α- and γ-globins may ameliorate these manifestations by mitigating sickle hemoglobin polymerization and erythrocyte sickling. BCL11A is a repressor of γ-globin expression and HbF production in adult erythrocytes. Its down-regulation is a promising therapeutic strategy for induction of HbF. METHODS We enrolled patients with sickle cell disease in a single-center, open-label pilot study. The investigational therapy involved infusion of autologous CD34+ cells transduced with the BCH-BB694 lentiviral vector, which encodes a short hairpin RNA (shRNA) targeting BCL11A mRNA embedded in a microRNA (shmiR), allowing erythroid lineage-specific knockdown. Patients were assessed for primary end points of engraftment and safety and for hematologic and clinical responses to treatment. RESULTS As of October 2020, six patients had been followed for at least 6 months after receiving BCH-BB694 gene therapy; median follow-up was 18 months (range, 7 to 29). All patients had engraftment, and adverse events were consistent with effects of the preparative chemotherapy. All the patients who could be fully evaluated achieved robust and stable HbF induction (percentage HbF/(F+S) at most recent follow-up, 20.4 to 41.3%), with HbF broadly distributed in red cells (F-cells 58.9 to 93.6% of untransfused red cells) and HbF per F-cell of 9.0 to 18.6 pg per cell. Clinical manifestations of sickle cell disease were reduced or absent during the follow-up period. CONCLUSIONS This study validates BCL11A inhibition as an effective target for HbF induction and provides preliminary evidence that shmiR-based gene knockdown offers a favorable risk-benefit profile in sickle cell disease. (Funded by the National Institutes of Health; ClinicalTrials.gov number, NCT03282656).
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Affiliation(s)
- Erica B Esrick
- From the Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School (E.B.E., L.E.L., A.B., C.B., M.F.C., B.M., K.B., S.-Y.P., W.B.L., C.D., M.M.H., D.A.W.), the Harvard Stem Cell Institute, Harvard Medical School (A.B., C.B.), the Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center (A.B., M.F.C., B.M., E.M., A.F., S.-Y.P., C.D., D.A.W.), the Division of Hematology, Brigham and Women's Hospital, Harvard Medical School (M. Achebe), the Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute (H.D., R.K., K.S., H.N., S.N., J.R.), the TransLab, Boston Children's Hospital (D.A., M. Armant), and the Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School (J.P.M.) - all in Boston; and Bluebird Bio, Cambridge, MA (O.N.)
| | - Leslie E Lehmann
- From the Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School (E.B.E., L.E.L., A.B., C.B., M.F.C., B.M., K.B., S.-Y.P., W.B.L., C.D., M.M.H., D.A.W.), the Harvard Stem Cell Institute, Harvard Medical School (A.B., C.B.), the Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center (A.B., M.F.C., B.M., E.M., A.F., S.-Y.P., C.D., D.A.W.), the Division of Hematology, Brigham and Women's Hospital, Harvard Medical School (M. Achebe), the Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute (H.D., R.K., K.S., H.N., S.N., J.R.), the TransLab, Boston Children's Hospital (D.A., M. Armant), and the Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School (J.P.M.) - all in Boston; and Bluebird Bio, Cambridge, MA (O.N.)
| | - Alessandra Biffi
- From the Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School (E.B.E., L.E.L., A.B., C.B., M.F.C., B.M., K.B., S.-Y.P., W.B.L., C.D., M.M.H., D.A.W.), the Harvard Stem Cell Institute, Harvard Medical School (A.B., C.B.), the Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center (A.B., M.F.C., B.M., E.M., A.F., S.-Y.P., C.D., D.A.W.), the Division of Hematology, Brigham and Women's Hospital, Harvard Medical School (M. Achebe), the Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute (H.D., R.K., K.S., H.N., S.N., J.R.), the TransLab, Boston Children's Hospital (D.A., M. Armant), and the Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School (J.P.M.) - all in Boston; and Bluebird Bio, Cambridge, MA (O.N.)
| | - Maureen Achebe
- From the Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School (E.B.E., L.E.L., A.B., C.B., M.F.C., B.M., K.B., S.-Y.P., W.B.L., C.D., M.M.H., D.A.W.), the Harvard Stem Cell Institute, Harvard Medical School (A.B., C.B.), the Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center (A.B., M.F.C., B.M., E.M., A.F., S.-Y.P., C.D., D.A.W.), the Division of Hematology, Brigham and Women's Hospital, Harvard Medical School (M. Achebe), the Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute (H.D., R.K., K.S., H.N., S.N., J.R.), the TransLab, Boston Children's Hospital (D.A., M. Armant), and the Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School (J.P.M.) - all in Boston; and Bluebird Bio, Cambridge, MA (O.N.)
| | - Christian Brendel
- From the Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School (E.B.E., L.E.L., A.B., C.B., M.F.C., B.M., K.B., S.-Y.P., W.B.L., C.D., M.M.H., D.A.W.), the Harvard Stem Cell Institute, Harvard Medical School (A.B., C.B.), the Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center (A.B., M.F.C., B.M., E.M., A.F., S.-Y.P., C.D., D.A.W.), the Division of Hematology, Brigham and Women's Hospital, Harvard Medical School (M. Achebe), the Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute (H.D., R.K., K.S., H.N., S.N., J.R.), the TransLab, Boston Children's Hospital (D.A., M. Armant), and the Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School (J.P.M.) - all in Boston; and Bluebird Bio, Cambridge, MA (O.N.)
| | - Marioara F Ciuculescu
- From the Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School (E.B.E., L.E.L., A.B., C.B., M.F.C., B.M., K.B., S.-Y.P., W.B.L., C.D., M.M.H., D.A.W.), the Harvard Stem Cell Institute, Harvard Medical School (A.B., C.B.), the Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center (A.B., M.F.C., B.M., E.M., A.F., S.-Y.P., C.D., D.A.W.), the Division of Hematology, Brigham and Women's Hospital, Harvard Medical School (M. Achebe), the Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute (H.D., R.K., K.S., H.N., S.N., J.R.), the TransLab, Boston Children's Hospital (D.A., M. Armant), and the Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School (J.P.M.) - all in Boston; and Bluebird Bio, Cambridge, MA (O.N.)
| | - Heather Daley
- From the Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School (E.B.E., L.E.L., A.B., C.B., M.F.C., B.M., K.B., S.-Y.P., W.B.L., C.D., M.M.H., D.A.W.), the Harvard Stem Cell Institute, Harvard Medical School (A.B., C.B.), the Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center (A.B., M.F.C., B.M., E.M., A.F., S.-Y.P., C.D., D.A.W.), the Division of Hematology, Brigham and Women's Hospital, Harvard Medical School (M. Achebe), the Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute (H.D., R.K., K.S., H.N., S.N., J.R.), the TransLab, Boston Children's Hospital (D.A., M. Armant), and the Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School (J.P.M.) - all in Boston; and Bluebird Bio, Cambridge, MA (O.N.)
| | - Brenda MacKinnon
- From the Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School (E.B.E., L.E.L., A.B., C.B., M.F.C., B.M., K.B., S.-Y.P., W.B.L., C.D., M.M.H., D.A.W.), the Harvard Stem Cell Institute, Harvard Medical School (A.B., C.B.), the Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center (A.B., M.F.C., B.M., E.M., A.F., S.-Y.P., C.D., D.A.W.), the Division of Hematology, Brigham and Women's Hospital, Harvard Medical School (M. Achebe), the Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute (H.D., R.K., K.S., H.N., S.N., J.R.), the TransLab, Boston Children's Hospital (D.A., M. Armant), and the Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School (J.P.M.) - all in Boston; and Bluebird Bio, Cambridge, MA (O.N.)
| | - Emily Morris
- From the Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School (E.B.E., L.E.L., A.B., C.B., M.F.C., B.M., K.B., S.-Y.P., W.B.L., C.D., M.M.H., D.A.W.), the Harvard Stem Cell Institute, Harvard Medical School (A.B., C.B.), the Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center (A.B., M.F.C., B.M., E.M., A.F., S.-Y.P., C.D., D.A.W.), the Division of Hematology, Brigham and Women's Hospital, Harvard Medical School (M. Achebe), the Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute (H.D., R.K., K.S., H.N., S.N., J.R.), the TransLab, Boston Children's Hospital (D.A., M. Armant), and the Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School (J.P.M.) - all in Boston; and Bluebird Bio, Cambridge, MA (O.N.)
| | - Amy Federico
- From the Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School (E.B.E., L.E.L., A.B., C.B., M.F.C., B.M., K.B., S.-Y.P., W.B.L., C.D., M.M.H., D.A.W.), the Harvard Stem Cell Institute, Harvard Medical School (A.B., C.B.), the Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center (A.B., M.F.C., B.M., E.M., A.F., S.-Y.P., C.D., D.A.W.), the Division of Hematology, Brigham and Women's Hospital, Harvard Medical School (M. Achebe), the Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute (H.D., R.K., K.S., H.N., S.N., J.R.), the TransLab, Boston Children's Hospital (D.A., M. Armant), and the Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School (J.P.M.) - all in Boston; and Bluebird Bio, Cambridge, MA (O.N.)
| | - Daniela Abriss
- From the Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School (E.B.E., L.E.L., A.B., C.B., M.F.C., B.M., K.B., S.-Y.P., W.B.L., C.D., M.M.H., D.A.W.), the Harvard Stem Cell Institute, Harvard Medical School (A.B., C.B.), the Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center (A.B., M.F.C., B.M., E.M., A.F., S.-Y.P., C.D., D.A.W.), the Division of Hematology, Brigham and Women's Hospital, Harvard Medical School (M. Achebe), the Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute (H.D., R.K., K.S., H.N., S.N., J.R.), the TransLab, Boston Children's Hospital (D.A., M. Armant), and the Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School (J.P.M.) - all in Boston; and Bluebird Bio, Cambridge, MA (O.N.)
| | - Kari Boardman
- From the Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School (E.B.E., L.E.L., A.B., C.B., M.F.C., B.M., K.B., S.-Y.P., W.B.L., C.D., M.M.H., D.A.W.), the Harvard Stem Cell Institute, Harvard Medical School (A.B., C.B.), the Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center (A.B., M.F.C., B.M., E.M., A.F., S.-Y.P., C.D., D.A.W.), the Division of Hematology, Brigham and Women's Hospital, Harvard Medical School (M. Achebe), the Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute (H.D., R.K., K.S., H.N., S.N., J.R.), the TransLab, Boston Children's Hospital (D.A., M. Armant), and the Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School (J.P.M.) - all in Boston; and Bluebird Bio, Cambridge, MA (O.N.)
| | - Radia Khelladi
- From the Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School (E.B.E., L.E.L., A.B., C.B., M.F.C., B.M., K.B., S.-Y.P., W.B.L., C.D., M.M.H., D.A.W.), the Harvard Stem Cell Institute, Harvard Medical School (A.B., C.B.), the Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center (A.B., M.F.C., B.M., E.M., A.F., S.-Y.P., C.D., D.A.W.), the Division of Hematology, Brigham and Women's Hospital, Harvard Medical School (M. Achebe), the Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute (H.D., R.K., K.S., H.N., S.N., J.R.), the TransLab, Boston Children's Hospital (D.A., M. Armant), and the Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School (J.P.M.) - all in Boston; and Bluebird Bio, Cambridge, MA (O.N.)
| | - Kit Shaw
- From the Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School (E.B.E., L.E.L., A.B., C.B., M.F.C., B.M., K.B., S.-Y.P., W.B.L., C.D., M.M.H., D.A.W.), the Harvard Stem Cell Institute, Harvard Medical School (A.B., C.B.), the Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center (A.B., M.F.C., B.M., E.M., A.F., S.-Y.P., C.D., D.A.W.), the Division of Hematology, Brigham and Women's Hospital, Harvard Medical School (M. Achebe), the Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute (H.D., R.K., K.S., H.N., S.N., J.R.), the TransLab, Boston Children's Hospital (D.A., M. Armant), and the Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School (J.P.M.) - all in Boston; and Bluebird Bio, Cambridge, MA (O.N.)
| | - Helene Negre
- From the Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School (E.B.E., L.E.L., A.B., C.B., M.F.C., B.M., K.B., S.-Y.P., W.B.L., C.D., M.M.H., D.A.W.), the Harvard Stem Cell Institute, Harvard Medical School (A.B., C.B.), the Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center (A.B., M.F.C., B.M., E.M., A.F., S.-Y.P., C.D., D.A.W.), the Division of Hematology, Brigham and Women's Hospital, Harvard Medical School (M. Achebe), the Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute (H.D., R.K., K.S., H.N., S.N., J.R.), the TransLab, Boston Children's Hospital (D.A., M. Armant), and the Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School (J.P.M.) - all in Boston; and Bluebird Bio, Cambridge, MA (O.N.)
| | - Olivier Negre
- From the Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School (E.B.E., L.E.L., A.B., C.B., M.F.C., B.M., K.B., S.-Y.P., W.B.L., C.D., M.M.H., D.A.W.), the Harvard Stem Cell Institute, Harvard Medical School (A.B., C.B.), the Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center (A.B., M.F.C., B.M., E.M., A.F., S.-Y.P., C.D., D.A.W.), the Division of Hematology, Brigham and Women's Hospital, Harvard Medical School (M. Achebe), the Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute (H.D., R.K., K.S., H.N., S.N., J.R.), the TransLab, Boston Children's Hospital (D.A., M. Armant), and the Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School (J.P.M.) - all in Boston; and Bluebird Bio, Cambridge, MA (O.N.)
| | - Sarah Nikiforow
- From the Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School (E.B.E., L.E.L., A.B., C.B., M.F.C., B.M., K.B., S.-Y.P., W.B.L., C.D., M.M.H., D.A.W.), the Harvard Stem Cell Institute, Harvard Medical School (A.B., C.B.), the Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center (A.B., M.F.C., B.M., E.M., A.F., S.-Y.P., C.D., D.A.W.), the Division of Hematology, Brigham and Women's Hospital, Harvard Medical School (M. Achebe), the Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute (H.D., R.K., K.S., H.N., S.N., J.R.), the TransLab, Boston Children's Hospital (D.A., M. Armant), and the Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School (J.P.M.) - all in Boston; and Bluebird Bio, Cambridge, MA (O.N.)
| | - Jerome Ritz
- From the Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School (E.B.E., L.E.L., A.B., C.B., M.F.C., B.M., K.B., S.-Y.P., W.B.L., C.D., M.M.H., D.A.W.), the Harvard Stem Cell Institute, Harvard Medical School (A.B., C.B.), the Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center (A.B., M.F.C., B.M., E.M., A.F., S.-Y.P., C.D., D.A.W.), the Division of Hematology, Brigham and Women's Hospital, Harvard Medical School (M. Achebe), the Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute (H.D., R.K., K.S., H.N., S.N., J.R.), the TransLab, Boston Children's Hospital (D.A., M. Armant), and the Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School (J.P.M.) - all in Boston; and Bluebird Bio, Cambridge, MA (O.N.)
| | - Sung-Yun Pai
- From the Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School (E.B.E., L.E.L., A.B., C.B., M.F.C., B.M., K.B., S.-Y.P., W.B.L., C.D., M.M.H., D.A.W.), the Harvard Stem Cell Institute, Harvard Medical School (A.B., C.B.), the Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center (A.B., M.F.C., B.M., E.M., A.F., S.-Y.P., C.D., D.A.W.), the Division of Hematology, Brigham and Women's Hospital, Harvard Medical School (M. Achebe), the Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute (H.D., R.K., K.S., H.N., S.N., J.R.), the TransLab, Boston Children's Hospital (D.A., M. Armant), and the Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School (J.P.M.) - all in Boston; and Bluebird Bio, Cambridge, MA (O.N.)
| | - Wendy B London
- From the Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School (E.B.E., L.E.L., A.B., C.B., M.F.C., B.M., K.B., S.-Y.P., W.B.L., C.D., M.M.H., D.A.W.), the Harvard Stem Cell Institute, Harvard Medical School (A.B., C.B.), the Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center (A.B., M.F.C., B.M., E.M., A.F., S.-Y.P., C.D., D.A.W.), the Division of Hematology, Brigham and Women's Hospital, Harvard Medical School (M. Achebe), the Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute (H.D., R.K., K.S., H.N., S.N., J.R.), the TransLab, Boston Children's Hospital (D.A., M. Armant), and the Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School (J.P.M.) - all in Boston; and Bluebird Bio, Cambridge, MA (O.N.)
| | - Colleen Dansereau
- From the Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School (E.B.E., L.E.L., A.B., C.B., M.F.C., B.M., K.B., S.-Y.P., W.B.L., C.D., M.M.H., D.A.W.), the Harvard Stem Cell Institute, Harvard Medical School (A.B., C.B.), the Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center (A.B., M.F.C., B.M., E.M., A.F., S.-Y.P., C.D., D.A.W.), the Division of Hematology, Brigham and Women's Hospital, Harvard Medical School (M. Achebe), the Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute (H.D., R.K., K.S., H.N., S.N., J.R.), the TransLab, Boston Children's Hospital (D.A., M. Armant), and the Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School (J.P.M.) - all in Boston; and Bluebird Bio, Cambridge, MA (O.N.)
| | - Matthew M Heeney
- From the Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School (E.B.E., L.E.L., A.B., C.B., M.F.C., B.M., K.B., S.-Y.P., W.B.L., C.D., M.M.H., D.A.W.), the Harvard Stem Cell Institute, Harvard Medical School (A.B., C.B.), the Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center (A.B., M.F.C., B.M., E.M., A.F., S.-Y.P., C.D., D.A.W.), the Division of Hematology, Brigham and Women's Hospital, Harvard Medical School (M. Achebe), the Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute (H.D., R.K., K.S., H.N., S.N., J.R.), the TransLab, Boston Children's Hospital (D.A., M. Armant), and the Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School (J.P.M.) - all in Boston; and Bluebird Bio, Cambridge, MA (O.N.)
| | - Myriam Armant
- From the Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School (E.B.E., L.E.L., A.B., C.B., M.F.C., B.M., K.B., S.-Y.P., W.B.L., C.D., M.M.H., D.A.W.), the Harvard Stem Cell Institute, Harvard Medical School (A.B., C.B.), the Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center (A.B., M.F.C., B.M., E.M., A.F., S.-Y.P., C.D., D.A.W.), the Division of Hematology, Brigham and Women's Hospital, Harvard Medical School (M. Achebe), the Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute (H.D., R.K., K.S., H.N., S.N., J.R.), the TransLab, Boston Children's Hospital (D.A., M. Armant), and the Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School (J.P.M.) - all in Boston; and Bluebird Bio, Cambridge, MA (O.N.)
| | - John P Manis
- From the Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School (E.B.E., L.E.L., A.B., C.B., M.F.C., B.M., K.B., S.-Y.P., W.B.L., C.D., M.M.H., D.A.W.), the Harvard Stem Cell Institute, Harvard Medical School (A.B., C.B.), the Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center (A.B., M.F.C., B.M., E.M., A.F., S.-Y.P., C.D., D.A.W.), the Division of Hematology, Brigham and Women's Hospital, Harvard Medical School (M. Achebe), the Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute (H.D., R.K., K.S., H.N., S.N., J.R.), the TransLab, Boston Children's Hospital (D.A., M. Armant), and the Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School (J.P.M.) - all in Boston; and Bluebird Bio, Cambridge, MA (O.N.)
| | - David A Williams
- From the Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School (E.B.E., L.E.L., A.B., C.B., M.F.C., B.M., K.B., S.-Y.P., W.B.L., C.D., M.M.H., D.A.W.), the Harvard Stem Cell Institute, Harvard Medical School (A.B., C.B.), the Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center (A.B., M.F.C., B.M., E.M., A.F., S.-Y.P., C.D., D.A.W.), the Division of Hematology, Brigham and Women's Hospital, Harvard Medical School (M. Achebe), the Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute (H.D., R.K., K.S., H.N., S.N., J.R.), the TransLab, Boston Children's Hospital (D.A., M. Armant), and the Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School (J.P.M.) - all in Boston; and Bluebird Bio, Cambridge, MA (O.N.)
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48
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Wang Z, Wang P, Li Y, Peng H, Zhu Y, Mohandas N, Liu J. Interplay between cofactors and transcription factors in hematopoiesis and hematological malignancies. Signal Transduct Target Ther 2021; 6:24. [PMID: 33468999 PMCID: PMC7815747 DOI: 10.1038/s41392-020-00422-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/16/2020] [Accepted: 10/26/2020] [Indexed: 02/07/2023] Open
Abstract
Hematopoiesis requires finely tuned regulation of gene expression at each stage of development. The regulation of gene transcription involves not only individual transcription factors (TFs) but also transcription complexes (TCs) composed of transcription factor(s) and multisubunit cofactors. In their normal compositions, TCs orchestrate lineage-specific patterns of gene expression and ensure the production of the correct proportions of individual cell lineages during hematopoiesis. The integration of posttranslational and conformational modifications in the chromatin landscape, nucleosomes, histones and interacting components via the cofactor–TF interplay is critical to optimal TF activity. Mutations or translocations of cofactor genes are expected to alter cofactor–TF interactions, which may be causative for the pathogenesis of various hematologic disorders. Blocking TF oncogenic activity in hematologic disorders through targeting cofactors in aberrant complexes has been an exciting therapeutic strategy. In this review, we summarize the current knowledge regarding the models and functions of cofactor–TF interplay in physiological hematopoiesis and highlight their implications in the etiology of hematological malignancies. This review presents a deep insight into the physiological and pathological implications of transcription machinery in the blood system.
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Affiliation(s)
- Zi Wang
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, 410011, ChangSha, Hunan, China. .,Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, 410078, Changsha, Hunan, China.
| | - Pan Wang
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, 410078, Changsha, Hunan, China
| | - Yanan Li
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, 410078, Changsha, Hunan, China
| | - Hongling Peng
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, 410011, ChangSha, Hunan, China
| | - Yu Zhu
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, 410078, Changsha, Hunan, China
| | - Narla Mohandas
- Red Cell Physiology Laboratory, New York Blood Center, New York, NY, USA
| | - Jing Liu
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, 410078, Changsha, Hunan, China.
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49
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Papizan JB, Porter SN, Sharma A, Pruett-Miller SM. Therapeutic gene editing strategies using CRISPR-Cas9 for the β-hemoglobinopathies. J Biomed Res 2021; 35:115-134. [PMID: 33349624 PMCID: PMC8038529 DOI: 10.7555/jbr.34.20200096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
With advancements in gene editing technologies, our ability to make precise and efficient modifications to the genome is increasing at a remarkable rate, paving the way for scientists and clinicians to uniquely treat a multitude of previously irremediable diseases. CRISPR-Cas9, short for clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9, is a gene editing platform with the ability to alter the nucleotide sequence of the genome in living cells. This technology is increasing the number and pace at which new gene editing treatments for genetic disorders are moving toward the clinic. The β-hemoglobinopathies are a group of monogenic diseases, which despite their high prevalence and chronic debilitating nature, continue to have few therapeutic options available. In this review, we will discuss our existing comprehension of the genetics and current state of treatment for β-hemoglobinopathies, consider potential genome editing therapeutic strategies, and provide an overview of the current state of clinical trials using CRISPR-Cas9 gene editing.
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Affiliation(s)
- James B Papizan
- Department of Cellular and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.,Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shaina N Porter
- Department of Cellular and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.,Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Akshay Sharma
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shondra M Pruett-Miller
- Department of Cellular and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.,Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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50
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Demirci S, Zeng J, Wu Y, Uchida N, Shen AH, Pellin D, Gamer J, Yapundich M, Drysdale C, Bonanno J, Bonifacino AC, Krouse AE, Linde NS, Engels T, Donahue RE, Haro-Mora JJ, Leonard A, Nassehi T, Luk K, Porter SN, Lazzarotto CR, Tsai SQ, Weiss MJ, Pruett-Miller SM, Wolfe SA, Bauer DE, Tisdale JF. BCL11A enhancer-edited hematopoietic stem cells persist in rhesus monkeys without toxicity. J Clin Invest 2020; 130:6677-6687. [PMID: 32897878 PMCID: PMC7685754 DOI: 10.1172/jci140189] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/02/2020] [Indexed: 12/11/2022] Open
Abstract
Gene editing of the erythroid-specific BCL11A enhancer in hematopoietic stem and progenitor cells (HSPCs) from patients with sickle cell disease (SCD) induces fetal hemoglobin (HbF) without detectable toxicity, as assessed by mouse xenotransplant. Here, we evaluated autologous engraftment and HbF induction potential of erythroid-specific BCL11A enhancer-edited HSPCs in 4 nonhuman primates. We used a single guide RNA (sgRNA) with identical human and rhesus target sequences to disrupt a GATA1 binding site at the BCL11A +58 erythroid enhancer. Cas9 protein and sgRNA ribonucleoprotein complex (RNP) was electroporated into rhesus HSPCs, followed by autologous infusion after myeloablation. We found that gene edits persisted in peripheral blood (PB) and bone marrow (BM) for up to 101 weeks similarly for BCL11A enhancer- or control locus-targeted (AAVS1-targeted) cells. Biallelic BCL11A enhancer editing resulted in robust γ-globin induction, with the highest levels observed during stress erythropoiesis. Indels were evenly distributed across PB and BM lineages. Off-target edits were not observed. Nonhomologous end-joining repair alleles were enriched in engrafting HSCs. In summary, we found that edited HSCs can persist for at least 101 weeks after transplant and biallelic-edited HSCs provide substantial HbF levels in PB red blood cells, together supporting further clinical translation of this approach.
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Affiliation(s)
- Selami Demirci
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Jing Zeng
- Division of Hematology/Oncology, Boston Children’s Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Department of Pediatrics, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Yuxuan Wu
- Division of Hematology/Oncology, Boston Children’s Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Department of Pediatrics, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, Massachusetts, USA
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Naoya Uchida
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Anne H. Shen
- Division of Hematology/Oncology, Boston Children’s Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Department of Pediatrics, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Danilo Pellin
- Gene Therapy Program, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Jackson Gamer
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Morgan Yapundich
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Claire Drysdale
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Jasmine Bonanno
- Division of Hematology/Oncology, Boston Children’s Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Department of Pediatrics, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Allen E. Krouse
- Translational Stem Cell Biology Branch, NHLBI, NIH, Bethesda, Maryland, USA
| | - Nathaniel S. Linde
- Translational Stem Cell Biology Branch, NHLBI, NIH, Bethesda, Maryland, USA
| | - Theresa Engels
- Translational Stem Cell Biology Branch, NHLBI, NIH, Bethesda, Maryland, USA
| | - Robert E. Donahue
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Juan J. Haro-Mora
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Alexis Leonard
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Tina Nassehi
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Kevin Luk
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Shaina N. Porter
- Department of Cell and Molecular Biology, Center for Advanced Genome Engineering, and
| | - Cicera R. Lazzarotto
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Shengdar Q. Tsai
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Mitchell J. Weiss
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | | | - Scot A. Wolfe
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Daniel E. Bauer
- Division of Hematology/Oncology, Boston Children’s Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Department of Pediatrics, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - John F. Tisdale
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
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